tag:blogger.com,1999:blog-222503362023-11-16T07:47:19.415+00:00Evo-KarmaAll about the good, the bad and the ugly things in life but mainly stuff about evolution, diversity of life, life forms and morphogenesis, phylogenies, trees and insects. Lots of biological news and comments. Cool discoveries of new species etc...blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.comBlogger101125tag:blogger.com,1999:blog-22250336.post-88720218152191844472012-12-21T14:01:00.001+00:002012-12-21T14:01:17.913+00:00Mobile Lab Management System<table cellpadding="0" cellspacing="0" class="tr-caption-container zemanta-img" style="float: right; margin-right: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.flickr.com/photos/24801682@N08/2978231012" imageanchor="1" style="margin-bottom: 1em; margin-left: auto; margin-right: auto; text-align: clear:right;"><img alt="LaBLog on a tablet in the lab" border="0" class="zemanta-img-inserted" height="240" src="http://farm4.static.flickr.com/3067/2978231012_5f2c3b5826_m.jpg" style="border: none; font-size: 0.8em;" width="180" /></a></td></tr>
<tr><td class="tr-caption zemanta-img-attribution" style="text-align: center;">LaBLog on a tablet in the lab (Photo credit: <a href="http://www.flickr.com/photos/24801682@N08/2978231012" target="_blank">cameronneylon</a>)</td></tr>
</tbody></table>
When I first started working in <a class="g-profile" href="http://plus.google.com/104270512787685766370" target="_blank">+Roderic D. M. Page</a> lab, I was fortunate that <a class="g-profile" href="http://plus.google.com/102823825937391928648" target="_blank">+Vincent Smith</a> had been looking after the frozen collection of lice. He had inventoried and stored all the different specimens in carefully labelled tubes and boxes. The collection had been carefully built up and catalogued by a number of previous members in Rod's lab in a database called Lousebase. I was lucky because it made it very easy to find the samples I wanted to work on. <br />
Lousebase went through a number of versions, originating from multiple excel spreadsheets used independently by the group, then it was compiled into an Access database, then it made it onto the web via ColdFusion with an underlying <a class="zem_slink" href="http://www.iso.org/iso/catalogue_detail.htm?csnumber=45498" rel="homepage" target="_blank" title="SQL">SQL database</a>. When ColdFusion stopped playing nice, I made an attempt to write some PHP to interface with the SQL database but finally transferred everything into <a class="zem_slink" href="http://docs.google.com/" rel="homepage" target="_blank" title="Google Docs">GoogleDocs</a> <a href="http://goo.gl/6ilXf" target="_blank">here</a>.<br />
<br />
Working in the molecular lab which was two flights of stairs up from the office, certainly kept me fit but I dreamt of the day when I could interface with the database via a mobile device, so I put forward a project for an MSc Computer Science student to build such an app to interface with LouseBase on GoogleDocs. Here is a presentation I gave explaining what Nachiket Khandetod did for his MSc project.<br />
<br />
<iframe allowfullscreen="allowfullscreen" frameborder="0" height="356" marginheight="0" marginwidth="0" mozallowfullscreen="mozallowfullscreen" scrolling="no" src="http://www.slideshare.net/slideshow/embed_code/15725375" style="border-width: 1px 1px 0; border: 1px solid #CCC; margin-bottom: 5px;" webkitallowfullscreen="webkitallowfullscreen" width="427"> </iframe> <div style="margin-bottom: 5px;">
<strong> <a href="http://www.slideshare.net/josephhughes/mobile-lab-app" target="_blank" title="Mobile lab app">Mobile lab app</a> </strong> from <strong><a href="http://www.slideshare.net/josephhughes" target="_blank">josephhughes</a></strong> </div>
<br />
<br />
The main difficulties he encountered was dealing with the Google API and having multiple user accounts accessing the same spreadsheet. At the end of the project, he said that it would have been much easier to link directly to an SQL database. However, he still managed to produce an Android app that updated a <a class="zem_slink" href="http://docs.google.com/" rel="homepage" target="_blank" title="Google Docs">Google spreadsheet</a> and that multiple users could work on simultaneously as long as they used a single Google account. He also built data caching into the app so if someone was out of WiFi range, they could store the data to synchronize later. <br />
<br />
All the code for the app is open source and available on <a href="https://github.com/josephhughes/MicroApp" target="_blank">github</a> but it is not particularly well annotated. One day, when I have time, I will revisit this to build a mobile lab management system the way I think it should be done.<br />
<br />
Note:<br />
Unfortunately, the spreadsheet name and Google Account were hard coded into the app, for this reason you will need to change the email (xxx@xxx) and password (xxx) in the following files before creating the .apk:<br />
src/com/ei/auth/BasicAuthenticatorImpl.java<br />
src/com/ei/auth/Account.java<br />
<br />
Now that tablets are cheap and common place, it will not be long until they change the way we work, probably to a greater same extent than PCs have.<br />
<br />
<div class="zemanta-pixie" style="height: 15px; margin-top: 10px;">
<a class="zemanta-pixie-a" href="http://www.zemanta.com/?px" title="Enhanced by Zemanta"><img alt="Enhanced by Zemanta" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=36e3887b-b749-4acd-8493-2ffa758d7df6" style="border: none; float: right;" /></a></div>
blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com1tag:blogger.com,1999:blog-22250336.post-31202053527313977122012-10-25T19:38:00.000+00:002012-10-25T19:38:13.393+00:00mini tablet comparison: Google versus Amazon versus Apple<table cellpadding="0" cellspacing="0" class="tr-caption-container zemanta-img" style="color: black; float: right; margin-right: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.flickr.com/photos/66579785@N00/7792605500" imageanchor="1" style="margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt="Nexus 7 Home" border="0" class="zemanta-img-inserted" height="240" src="http://farm9.static.flickr.com/8421/7792605500_92cb076139_m.jpg" style="border: medium none; font-size: 0.8em;" width="160" /></a></td></tr>
<tr><td class="tr-caption zemanta-img-attribution" style="text-align: center; width: 160px;">Nexus 7 Home (Photo credit: <a href="http://www.flickr.com/photos/66579785@N00/7792605500" target="_blank">Stmpjmpr</a>)</td></tr>
</tbody></table>
<div style="color: black;">
I've just done a little table to compare the Nexus 7, <a class="zem_slink" href="http://www.amazon.com/kindlefire" rel="homepage" target="_blank" title="Kindle Fire">Kindle Fire</a> and <a class="zem_slink" href="http://www.apple.com/iphone" rel="homepage" target="_blank" title="iPhone">iPad mini</a> which I thought I would share. </div>
<div style="color: black;">
Off course, it is not all about the specs, it is also about the look and feel of the mini-tablet and mainly about the ecosystem that you want to buy into: Google versus Amazon versus Apple. <br />I feel that these ecosystems are getting increasingly incompatible with one another and changing from one ecosystem to another can be painful and requires a lot of adaptation.</div>
<div style="color: black;">
<br /></div>
<table border="1" cellpadding="0" cellspacing="0" class="MsoNormalTable" style="border-collapse: collapse; border: medium none; color: black;">
<tbody>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Nexus 7 <o:p></o:p></span></div>
</td>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Kindel</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> Fire<o:p></o:p></span></div>
</td>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">iPad</span></span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> mini<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Screen<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Ppi</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> (pixel per inch)<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">7" <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">1280x800 HD display at <b>216 <span class="SpellE">ppi</span></b><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">7" multi-touch, <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">1024x600 resolution <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">at</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> 169 <span class="SpellE">ppi</span> <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">or</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> 1280x800 resolution for the HD option<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<b><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">7.9"</span></b><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> <span class="SpellE">multi</span>-touch,
<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">1024x768 resolution at 163 <span class="SpellE">ppi</span>
<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Front facing camera<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">1.2MP <o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">front</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">-facing camera<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">1.2MP <span class="SpellE">FaceTime</span> HD
camera <o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Weight in grams<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">340g<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">400g</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><b>308g</b><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">312 (<span class="SpellE">wifi</span> + cellular)</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Memory<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><b>1 GB RAM</b><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal">
<span style="background: none repeat scroll 0% 0% rgb(255, 255, 255); font-family: Helvetica; font-size: 10pt;">512MB</span><span style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">512 MB (???)<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Battery<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">4325 <span class="SpellE">mAh</span> (Up to 8 hours
of active use)<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Up to 9 hours of reading, surfing the web on
Wi-Fi, watching video, or listening to music. </span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Up to 10 hours of surfing the web on
Wi-Fi, watching video or listening to music</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">CPU<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Quad-core <span class="SpellE">Tegra</span> 3
processor<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal">
<span style="background: none repeat scroll 0% 0% rgb(255, 255, 255); font-family: Helvetica; font-size: 10pt;">1GHz
dual-core processor</span><span style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<b><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Dual-core A5</span></b><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">
but see <a href="http://9to5mac.com/2012/03/30/benchmarked-new-ipads-a5x-vs-ipad-2s-a5-vs-tegra-3/" target="_blank">here</a> for full benchmarking<o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Size in mm<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">198.5 x 120 x 10.45<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">189 x 120 x 11.5 </span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><b>200 x 134.7 x 7.2</b> </span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Wireless<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">WiFi</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> 802.11 b/g/n + Bluetooth<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Wi-Fi (802.11a/b/g/n); does not support
connecting to ad-hoc (or peer-to-peer) Wi-Fi networks</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Wi-Fi (802.11a/b/g/n; 802.11n on 2.4GHz
and 5GHz)<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Bluetooth 4.0 technology</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Connection<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Micro USB<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">USB 2.0 (micro-B connector) port for connection
to a PC or Macintosh computer or to connect to the Kindle <span class="SpellE">PowerFast</span>
charging accessory</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Ligthning</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> <span class="SpellE">conector</span><o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">OS<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Android 4.1 (Jelly Bean)<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal">
<span style="font-family: Helvetica; font-size: 10pt;"><a href="http://en.wikipedia.org/wiki/Android_%28operating_system%29"><span style="text-decoration: none;">Android</span></a></span><span style="font-family: Helvetica; font-size: 10pt;"> 2.3
Gingerbread OS</span><span style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">iOS6</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Features<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Microphone<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">NFC (Android Beam)<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Accelerometer<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">GPS<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Magnetometer<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Gyroscope<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">3.5 mm stereo jack and integrated stereo
speakers</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">720p HD video<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">FaceTime</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> video calling <span class="SpellE">over Wi-Fi</span> or a mobile network</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">3</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Face detection<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Backside illumination<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="SpellE"><span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">iSight</span></span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">
camera<o:p></o:p> </span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">5MP
photos</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Autofocus<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Face detection<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Backside illumination<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Five-element lens<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Hybrid IR filter<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">ƒ/2.4 aperture<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 7pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 7pt;">
<span class="SpellE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Siri</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> - </span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Use your
voice to send messages, set reminders and more.<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<br /></div>
</td>
</tr>
<tr>
<td style="border: 1pt solid gray; padding: 0cm 5.4pt; width: 65.05pt;" valign="top" width="65"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Price<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 103.4pt;" valign="top" width="103"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£199 for 16GB and £159 for 6Gb<o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 92.1pt;" valign="top" width="92"><div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">8 GB internal memory, approximately 5.5GB
available for user content<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<b><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£129<o:p></o:p></span></b></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span class="GramE"><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">or</span></span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"> <b>£169</b>
for Fire HD with </span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">16
GB or £209 32 GB on device</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
</td>
<td style="border-color: -moz-use-text-color gray gray -moz-use-text-color; border-style: none solid solid none; border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 4cm;" valign="top" width="113"><div class="MsoNormal" style="margin-bottom: 7pt;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Wi-Fi</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">16GB<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£269</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">32GB<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£349</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">64GB<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£429</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 7pt;">
<br /></div>
<div class="MsoNormal" style="margin-bottom: 7pt;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">Wi-Fi
+ Cellular</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">16GB<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£369</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">32GB<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£449</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">64GB<o:p></o:p></span></div>
<div class="MsoNormal" style="margin-bottom: 0cm;">
<span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">£529 </span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;"><o:p></o:p></span></div>
<div align="center" class="MsoNormal" style="margin-bottom: 0cm; text-align: center;">
<br /></div>
</td>
</tr>
</tbody></table>
<div style="color: black;">
<br /></div>
<div class="zemanta-pixie" style="color: black; height: 15px; margin-top: 10px;">
<a class="zemanta-pixie-a" href="http://www.zemanta.com/?px" title="Enhanced by Zemanta"><img alt="Enhanced by Zemanta" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=871f3a1d-1cf9-4d4d-91d1-1201686833d9" style="border: medium none; float: right;" /></a></div>
blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com1tag:blogger.com,1999:blog-22250336.post-25321139785642930372012-05-25T19:45:00.000+00:002012-05-25T19:45:05.766+00:00Four years to digitise the phylogenies published so far!<table cellpadding="0" cellspacing="0" class="tr-caption-container zemanta-img" style="float: right; margin-right: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><div class="zemanta-img">
<a href="http://commons.wikipedia.org/wiki/File:Haeckel_arbol_bn.png" imageanchor="1" style="margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img alt=""Monophyletic tree of organisms". Er..." border="0" class="zemanta-img-inserted" height="466" src="http://upload.wikimedia.org/wikipedia/commons/thumb/b/bc/Haeckel_arbol_bn.png/300px-Haeckel_arbol_bn.png" style="border: medium none; font-size: 0.8em;" width="300" /></a></div>
</td></tr>
<tr><td class="tr-caption zemanta-img-attribution" style="text-align: center; width: 300px;">"Monophyletic tree of organisms". Ernst Haeckel: Generelle Morphologie der Organismen, etc. Berlin, 1866. (Photo credit: <a href="http://commons.wikipedia.org/wiki/File:Haeckel_arbol_bn.png" target="_blank">Wikipedia</a>)</td></tr>
</tbody></table>
<div style="text-align: right;">
</div>
<div style="text-align: right;">
</div>
Phylogenetic knowledge is being squandered at a rate of approximately 20,000 <a class="zem_slink" href="http://en.wikipedia.org/wiki/Phylogenetics" rel="wikipedia" target="_blank" title="Phylogenetics">phylogenies</a> a year (assuming that all papers with phylogen* in the title or abstract have illustrations of phylogenies). Fortunately, this loss of knowledge (and wasted money) is being tackled from multiple angles. On the one hand there is the <a class="zem_slink" href="http://en.wikipedia.org/wiki/Open_Access_movement" rel="wikipedia" target="_blank" title="Open Access movement">open access movement</a> that is striving to make publically-funded science freely available and accessible to everyone. For phylogenies this will hopefully go hand in hand with a greater submission of phylogenies to databases like TreeBASE. On the other, there are efforts to digitize past phylogenies: <a href="http://www.biomedcentral.com/1471-2105/12/178/abstract" target="_blank">TreeRipper</a>, TreeSnatcher and now <a href="http://www.biomedcentral.com/1471-2105/13/110/abstract" target="_blank">TreeSnatcher Plus</a>.<br />
<br />
TreeSnatcher Plus has recently made a number of improvements on its predecessor and it was great to see that they benchmarked it against the same dataset as TreeRipper which contained phylogenies from the open access <a class="zem_slink" href="http://en.wikipedia.org/wiki/BMC_journals" rel="wikipedia" target="_blank" title="BMC journals">BMC Evolutionary Biology</a>. They state that the average time for processing was 160s per phylogeny. I was interested to see how long it would take to digitise all the phylogenies produced to date. Assuming that all papers with phylogen* in the title has an image of a phylogeny, there are 734,585 published phylogenies according to ISI Web of Knowledge, that would require 4 years to digitise. The result might not be so bleak if <a class="zem_slink" href="http://www.ncbi.nlm.nih.gov/pubmed/" rel="homepage" target="_blank" title="PubMed">Pubmed</a> represents a more accurate number of phylogenies: 131,659 articles which would require a little under 1 year to digitise semi-automatically. <br />
<br />
O.K. these numbers a pie in the sky but can we afford this wasted time?<br />
<div class="zemanta-pixie" style="height: 15px; margin-top: 10px;">
<a class="zemanta-pixie-a" href="http://www.zemanta.com/?px" title="Enhanced by Zemanta"><img alt="Enhanced by Zemanta" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=0969a851-018c-4e0d-ada2-c152f02e9007" style="border: medium none; float: right;" /></a></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-1707141640265365322012-04-19T16:06:00.002+00:002012-04-19T16:06:29.372+00:00Crowdsourcing science project for phylogenies?<span class="zemanta-img separator" style="clear: right;"><a href="http://commons.wikipedia.org/wiki/File:Crowd_in_HK.JPG" style="clear: right; display: block; float: right; margin-left: 1em; margin-right: 1em;"><img alt="from en wp :http://en.wikipedia.org/wiki/Image..." height="199" src="http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Crowd_in_HK.JPG/300px-Crowd_in_HK.JPG" style="border: medium none; font-size: 0.8em;" width="300" /></a><span class="zemanta-img-attribution" style="clear: both; float: right; margin-left: 1em; margin-right: 1em; width: 300px;">Image via <a href="http://commons.wikipedia.org/wiki/File:Crowd_in_HK.JPG">Wikipedia</a></span></span>The idea behind crowdsourcing is that the answer to a question is often more likely to be correct if you average the answers from a large number of non-experts rather than a single expert in the field. The term "crowdsourcing" has also been used for projects that outsource repetitive or challenging work to a crowd via the internet.<br />
I have been thinking of outsourcing the problem of conversion of embedded phylogenies in PDFs back to newick/nexus format and have been looking at various science projects that have used crowdsourcing.<br />
<br />
The most impressive from my point of view is <a href="http://www.galaxyzoo.org/">Galaxy Zoo</a> which has already resulted in a number of publications and impressive discoveries. Astrophysicist use the crowd to categorise 1000s of galaxies and have expanded the crowd tasks to include matching images of galaxies with randomly simulated images.<br />
<br />
<a href="http://stardustathome.ssl.berkeley.edu/about.php">Stardust@Home</a> is another astrophysics project which asks that the crowd looks through images for dust particles brought back to earth by a spacecraft in 2006.<br />
<br />
Another cool project is the <a href="http://opendino.wordpress.com/">Open Dinosaur Project</a> which asks that the crowd aggregates published measurements of dinosaur limb bones for many different taxa from the literature and directly measured from specimens to study the evolutionary transitions from bipedality to quadrupedality.<br />
<br />
<a href="http://fold.it/portal/">Foldit</a> is a computer game enabling the crowd to contribute to our understanding of how protein folds. Figuring out which of the many, many possible structures is the best one is regarded as one of the hardest problems in biology today and current methods take a lot of money and time, even for computers. The idea of using human's spare time to get further insight is genius!<br />
<br />
Another game that might not be directly relevant to science is <a href="http://images.google.com/imagelabeler/">Google Image Labeler</a> which I found rather addictive. Google gets users to label/tag images as a side-effect of playing a game and this is probably used to improve image searches on the web. I list it hear because I came across a few images of animals that in some cases were labeled down to the latin binomial.<br />
<br />
<span style="font-weight: bold;">UPDATE</span>: An interesting new crowd sourcing project at <a href="http://www.oldweather.org/">http://www.oldweather.org/</a> to help gather information about past climates from hand written nautical records.<br />
<div class="zemanta-pixie" style="height: 15px; margin-top: 10px;">
<a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img alt="Enhanced by Zemanta" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=78eaa7f7-5318-42c3-9cb8-e8fecc85e7a3" style="border: medium none; float: right;" /></a><span class="zem-script more-related pretty-attribution"><script defer="defer" src="http://static.zemanta.com/readside/loader.js" type="text/javascript">
</script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-48300620834601012662012-04-13T21:24:00.000+00:002012-04-13T21:24:59.908+00:00Share your trees and reduce your carbon footprint<div style="text-align: right;">
</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-Yeasb6_v37QOjrZ9XrMVs_dPw8ajWWwIp5O8sNxqyfftj9fXyI2kwDkdT7YpPLDU2Oik0DIf34dm6ku95azTPlNE_SLvwOphBXcNHTr2vQyBhyphenhyphenrk_UoYaQnpytl7dvGlyjmC/s1600/carbonPhylo.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" height="226" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj-Yeasb6_v37QOjrZ9XrMVs_dPw8ajWWwIp5O8sNxqyfftj9fXyI2kwDkdT7YpPLDU2Oik0DIf34dm6ku95azTPlNE_SLvwOphBXcNHTr2vQyBhyphenhyphenrk_UoYaQnpytl7dvGlyjmC/s320/carbonPhylo.jpg" width="320" /></a></div>
I recently attended the <a href="http://biology.st-andrews.ac.uk/cegg/spdg/" target="_blank">SPDG</a> in Glasgow. This is an discussion group on phylogenetics which takes place in various Universities across Scotland. The guest lecturer at the last meeting was <a href="http://www.exelixis-lab.org/" target="_blank">Alexandros Stamatakis</a> from Heidelberg. The main part of his talk was about the PaPaRa software which can be used to align short reads to a phylogeny. This is really useful for the identification of next-gen reads from environmental samples. However, he also talked about reducing the carbon footprint of computational biology by writing better algorithms and code. The effect of heavy computation on the environment was not new to me as I once sat through a video conference by Herve Philippe at the <a href="http://esa.confex.com/esa/2008/webprogram/Session7822.html" target="_blank">Entomological Society of America</a> which was meant to be about "phylogenomics and the sister groups to Hexapoda" but ended up being about why he hadn't travelled to Reno, Nevada. He made valid points, which can be found <a href="http://www.cell.com/trends/genetics/fulltext/S0168-9525(08)00109-1" target="_blank">here</a>. At the SPDG, we also had a video conference from <a href="http://matsen.fhcrc.org/" target="_blank">Erick Matsen</a> and fortunately this time it was on topic. Erick is the organiser of <a href="http://phyloseminar.org/" target="_blank">phyloseminar</a> which is well worth having a look at and could definitely lower your carbon footprint.<br />
<br />
More efficient algorithms and programming, videoconferencing! This all got me thinking about the three Rs: REDUCE, REUSE and RECYCLE in the context of phylogenetics. We can all do our bit to REDUCE our carbon footprint when doing phylogenetics. For starters, is the analysis I want to do really necessary, does it have to run as long, can we use a better, more efficient algorithms. Secondly, we can REUSE the trees that others have already done but this means that we need to get much better at sharing our trees. <a href="http://www.treebase.org/" target="_blank">TreeBASE</a> and <a href="http://datadryad.org/" target="_blank">DataDryad</a> are undoubtedly playing an important role in enabling us to share phylogenies and thus reduce our carbon footprint. However, as discussed in "<a href="http://dx.doi.org/10.1038/npre.2007.1028.1" target="_blank">Towards a taxonomically intelligent phylogenetic database</a>" by <a href="http://iphylo.blogspot.co.uk/" target="_blank">Rod Page</a> the pace at which we are publishing phylogenies is not being matched by the submissions to TreeBASE. This leaves us with the last option to RECYCLE our trees. This should only be a last resort but ends up happening most of the time. For this we need to get back to our raw materials, the sequences, which fortunately are more consistently shared in GenBank and redo the analyses.<br />
<br />
Hopefully, this time round the algorithm will produce less carbon and the data will be submitted to TreeBASE!<br />
<div class="zemanta-pixie" style="height: 15px; margin-top: 10px;">
<a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img alt="Enhanced by Zemanta" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=4365aeda-7ac3-443c-9f0b-7b88b87fe4a1" style="border: none; float: right;" /></a></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-32347662779280281902012-04-10T16:43:00.000+00:002012-04-10T16:43:25.393+00:00Phylogeny digitisationI was hunting around for further research on phylogeny image digitisation to see whether any advances had been made since I last <a href="http://www.biomedcentral.com/1471-2105/12/178/abstract" target="_blank">published on the topic</a> and to keep my <a href="http://evo-karma.blogspot.co.uk/2011/05/recognition-of-tree-images.html" target="_blank">previous pos</a>t up-to-date. The main reason behind all of this is to see whether there would be a faster way to digitise a bunch of images that are accumulating on my hard drive. I thought it would be cool to do something with the ripped phylogenies for the <a href="http://ievobio.org/challenge.html" target="_blank">iEvoBio Challenge</a> but my current set of trees only has a total of 2,000 leaves and I need 10,000.<br />
Anyway, I came across <a href="http://en.bioinformatyk.eu/contest-articles/phylodigm-phylogenetic-tree-digitalisation-manager.html" target="_blank">PHYLODIGM</a> in my searches which looks promising. Thomas Laubach has also done some further work on <a href="http://www.cs.uni-duesseldorf.de/AG/BI/Software/treesnatcher/" target="_blank">TreeSnatcher Plus</a> including using the benchmarking dataset from <a href="http://www.biomedcentral.com/1471-2105/12/178/abstract" target="_blank">TreeRipper</a> and a number of tree files found via Google searches. Additionally, he has released the source code under the GNU General Public License<span class="Apple-style-span" style="font-family: Arial, Helvetica, sans-serif; font-size: 12px; line-height: 18px;"><b style="margin-top: 0px;">.</b></span><br />
This all looks promising!!!blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-81107317032221774922012-02-17T21:35:00.000+00:002012-02-17T21:35:40.929+00:00Not too far away from Gattaca<div class="separator" style="clear: both; text-align: left;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdde_j4NDGer6KSBQ4510yO41GkvxWmxFS-Tsuavvc0_ZSPGRWUIxvWT6L0G3_PS9WmmcopzxrX056R6bTxkMzpO9uYEsd4gqmZ-Bry-C3-Eck3zLpOXXk8FHGE8KYi10CRlHd/s1600/323972150_3c4c873db2.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="213" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdde_j4NDGer6KSBQ4510yO41GkvxWmxFS-Tsuavvc0_ZSPGRWUIxvWT6L0G3_PS9WmmcopzxrX056R6bTxkMzpO9uYEsd4gqmZ-Bry-C3-Eck3zLpOXXk8FHGE8KYi10CRlHd/s320/323972150_3c4c873db2.jpg" width="320" /></a></div>
I once said jokingly to my brother that by 2020 we would be pretty close to being able to sequence a whole human genome the way they do it in the 1997 film Gattaca. Today with the press release from Oxford Nanopore it looks like we are one step closer. The most striking piece of kit is the cute MinIon, a USB stick you plug into your laptop and off you go sequencing. The sequencing approach and the concept of sequencing until you have found what you are looking for, is completely different to previous sequencing technologies. Forget about next-generation sequencing, this is revolutionary sequencing.
<br />
There's already a lot of coverage about Oxford nanopores press release and i found <a href="http://pathogenomics.bham.ac.uk/blog/2012/02/oxford-nanopore-megaton-announcement-why-do-you-need-a-machine-exclusive-interview-for-this-blog/">Nick Loman's blog</a> posts on the new technology interesting.<br />
<br />
<iframe allowfullscreen="" frameborder="0" height="300" mozallowfullscreen="" src="http://player.vimeo.com/video/36903904?title=0&byline=0&portrait=0" webkitallowfullscreen="" width="400"></iframe><br />
<a href="http://vimeo.com/36903904">"Run Until": DNA sequencing informatics on the GridION and MinION systems</a> from <a href="http://vimeo.com/user5318092">Oxford Nanopore</a> on <a href="http://vimeo.com/">Vimeo</a>.blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-71012141227798469582011-10-26T21:27:00.000+00:002011-10-27T18:56:20.661+00:00Hacking the JPEG/PDF tree formatJust back from giving a presentation at the <a href="http://biology.st-andrews.ac.uk/cegg/spdg/">Scottish Phylogenetic Discussion group</a> in Edinburgh. Nice mix of talks. I think I got a lot of people thinking and talking about the way we are doing things and how we could improve the way we do things. The slides are available on <a href="http://dx.doi.org/10.1038/npre.2011.6556.1">Nature Precedings</a> but it is a bit slow to load, so I have added it to slideshare as well.
<br />
<div style="width:425px" id="__ss_9894861"><strong style="display:block;margin:12px 0 4px"><a href="http://www.slideshare.net/josephhughes/hacking-the-jpegpdf-tree-format" title="Hacking the JPEG/PDF tree format">Hacking the JPEG/PDF tree format</a></strong><object id="__sse9894861" width="425" height="355"><param name="movie" value="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=hackingtrees-111026155636-phpapp01&stripped_title=hacking-the-jpegpdf-tree-format&userName=josephhughes" /><param name="allowFullScreen" value="true"/><param name="allowScriptAccess" value="always"/><embed name="__sse9894861" src="http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=hackingtrees-111026155636-phpapp01&stripped_title=hacking-the-jpegpdf-tree-format&userName=josephhughes" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="425" height="355"></embed></object><div style="padding:5px 0 12px">View more <a href="http://www.slideshare.net/">presentations</a> from <a href="http://www.slideshare.net/josephhughes">josephhughes</a>.</div></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-7802942597751399842011-06-08T14:27:00.008+00:002011-06-08T15:24:49.671+00:00The phyloscape changes quickly, we need to build a better way to keep track of it<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJJO5iBlMK2ib-_DMpi6ahSg0ifo3paCC8l26RdkA3oRieggV2k2FFzhxy4zcGvM63u-OwKo3pbsjf2A35NogKVeU-kN36l0HCDWczNHw1GyB3pxvM4kS_nWlDomPT0z0t1VAj/s1600/Willi_Hennig2.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 154px; height: 200px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJJO5iBlMK2ib-_DMpi6ahSg0ifo3paCC8l26RdkA3oRieggV2k2FFzhxy4zcGvM63u-OwKo3pbsjf2A35NogKVeU-kN36l0HCDWczNHw1GyB3pxvM4kS_nWlDomPT0z0t1VAj/s200/Willi_Hennig2.jpg" alt="" id="BLOGGER_PHOTO_ID_5615869017182421746" border="0" /></a><br />Since Hennig's 1969 major publication on the phylogeny of hexapod orders (Insecta + Entognatha), I have found more than 60 publications of phylogenies on the ordinal relationships within the group. Some may be re-analyses of the same data but it is still quite a large number of studies. Thirty-seven of these have been published in the last decade and this rapid change in the phylogenetic landscape of this group (and this is probably the case for many other lineages) is increasingly becoming hard to keep track of. Sure, you could do a regular Pubmed or WoS search for phylogen* + insecta but you then need to extract the phylogeny and put it in the context of previously published studies. Sure there are databases like <a href="http://www.treebase.org/">TreeBase</a> and <a href="http://phylota.net/">PhyLoTa</a> that provide ready-made phylogenetic reconstructions but the former has limited content and the latter has limited resolution at many nodes of interest. <div>It is important to have an up-to-date and complete image of the phylogenetic landscape of the groups we work on, even if the overall picture is blurry. This would provide a better idea of areas that require further taxonomic sampling and/or a larger number of characters to resolve the relationships of interest, it would also provide a valuable resource for comparative studies. For this to work, information needs to be integrated between different databases like <a href="http://phylota.net/">PhyLoTA</a>, <a href="http://www.treebase.org/">TreeBASE</a>, <a href="http://www.ncbi.nlm.nih.gov/genbank/">GenBank</a>, <a href="http://www.treefam.org/">Treefam</a> etc. in an automated fashion as well as defrosting phylogenetic reconstructions from previously published studies (see my previous <a href="http://evo-karma.blogspot.com/2011/05/recognition-of-tree-images.html">post</a>). Perhaps a simple repository of third-party phylogenetic reconstructions would help: submitter - publication reference - figure number - phylogeny (newick, nexus, phyloxml, nexml ....). Although would anybody submit data? Perhaps I need to think of a way to reward those that do/<br /><div><br /></div><div><br /><span style="font-weight:bold;">Reference</span><br /></div><div>Hennig, W. 1969. Die Stammesgeschichte der Insekten. Frankfurt am Main, Germany: Kramer.</div></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com5tag:blogger.com,1999:blog-22250336.post-76537457653351239572011-05-22T20:06:00.003+00:002011-06-10T12:26:29.077+00:00Recognition of tree images<div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjFZH7oC2AwSw8cbo1rl7fc9oOUnj5I8DmCfvgjwY80iWitpdI1gakVmqMn0DktJfi7FcmBs23PGJcZ5PJ5ztwOCKptMvS7r1ALbFP9QKV5Of_kCfO-Wsr09inaZvNRZaz-vFC/s1600/Shredder.png" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img style="float: left; margin: 0pt 10px 10px 0pt; cursor: pointer; width: 200px; height: 200px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjFZH7oC2AwSw8cbo1rl7fc9oOUnj5I8DmCfvgjwY80iWitpdI1gakVmqMn0DktJfi7FcmBs23PGJcZ5PJ5ztwOCKptMvS7r1ALbFP9QKV5Of_kCfO-Wsr09inaZvNRZaz-vFC/s200/Shredder.png" alt="" id="BLOGGER_PHOTO_ID_5607295360061904386" border="0" /></a></div><div><br /></div><div><br /></div><div>I have just published a program on the <a href="http://www.biomedcentral.com/1471-2105/12/178/">automated recognition of phylogenies from tree images</a>. First of all, I would like to apologise for the use of the word 'towards' in the title, I know that it is <a href="http://larsjuhljensen.wordpress.com/2011/05/20/analysis-toward-doing-science/">increasingly being</a> used and irritating to some. I just wanted to be honest in that this program does not succeed on all tree images but is a step in the right direction.</div><div><br /></div><div>I thought I would take the opportunity to post a few links to software that deals with the same problem. We have all been rather unorginal with names!</div><div><br /></div><div><a href="http://microbe.bio.indiana.edu:7131/soft/iubionew/molbio/evolution/phylo/TreeThief/main.html">TreeThief</a>:</div><div>To my knowledge, this was the first program that dealt with the problem of converting a phylogenetic image back to the more useful bracket format such as NEXUS or newick. It requires the user to click on tips and nodes in a specific order and type in the label at the tips. Unfortunately, this program only works on MacOS 9.</div><div><br /></div><div><a href="http://www.cibiv.at/software/treesnatcher/">TreeSnatcher</a>:</div><div>TreeSnatcher was a conceptual advance on TreeThief, relies heavily on Java libraries and is cross-platform. It requires a limited amount of input from the user, such as selecting the foreground and background and lets the user improve the quality of the extraction thanks to this interactivity.</div><div><br /></div><div><a href="http://www.cs.uni-duesseldorf.de/AG/BI/Software/treesnatcher/">TreeSnatcher Plus</a>:</div><div>TreeSnatcher Plus is an improvement on TreeSnatcher as it lets the user convert almost anything to a newick file, for example it works on radial tree images.</div><div><br /></div><div><a href="https://stat.ethz.ch/pipermail/r-sig-phylo/2010-October/000816.html">TreeRogue</a>:</div><div>TreeRogue is essentially the same concept as TreeThief and I have just come across this so unfortunately do not make reference to it in my paper (sorry). It uses an R script that converts coordinates to a tree file. These coordinates can be detected from an image by using <a href="http://www.arizona-software.ch/graphclick/">GraphClick</a>, which costs $8.</div><div><br /></div><div><a href="http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper">TreeRipper</a>:<span class="zemanta-img separator" style="clear: right;"><a href="http://commons.wikipedia.org/wiki/File:Imagemagick-logo.png" style="margin-left: 1em; margin-right: 1em; display: block; float: right; clear: right;"><img src="http://upload.wikimedia.org/wikipedia/commons/thumb/0/0d/Imagemagick-logo.png/300px-Imagemagick-logo.png" alt="Logo for ImageMagick" style="font-size: 0.8em; border: medium none;" width="300" height="310" /></a><span class="zemanta-img-attribution" style="margin-left: 1em; margin-right: 1em; clear: both; float: right; width: 300px;">Image via <a href="http://commons.wikipedia.org/wiki/File:Imagemagick-logo.png">Wikipedia</a></span></span></div><div>TreeRipper has been written in C++ and there is a version running on the website, the <a href="http://code.google.com/p/treeripper/">code</a> is available under GNU GPL v3. It uses heavily the C++ API to to ImageMagick image-processing library (<a href="http://www.imagemagick.org/script/magick++.php?ImageMagick=pft3l0u3g5fr86edmtggjdtvg4">Magick++</a>) and it uses <a href="http://code.google.com/p/tesseract-ocr/">Tessecract-ocr</a> to convert the leaf labels to text. This is a fully automated approach that unfortunately only works on a proportion of the tree images. You could for example use TreeRipper for batch processing a large number of trees and then use a semi-automated approach for the trees that weren't converted.</div><div><br /></div><div>There is still a lot of room for improvement and I am hoping that someone out there will make further progress on this interesting challenge.</div><div><br /></div><div>Of course, none of these programs would be necessary if we all shared our trees and this would only be possible if we had a useful phylogenetic standard <= this statement should please <a href="http://www.tdwg.org/homepage-news-item/article/tdwg-interest-group-on-phylogenetics-standards-now-official/">the TDWG Interest Group on Phylogenetic Standards</a> ;)</div><div><br /></div><div><b>Reference:</b></div><div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJu6YuJQNJCSnrDHqvpszfnLOJPGUyhxfIXmXrySiHnnWQDlwENVQE70VN2Kjz0IX6QNPXIUTY3fqSQ0xFJbnBhNFOP-d0CbIFG8jcBzXlkh2QWvHUF2aROLCDr4285eqOeeh4/s1600/highlyaccessed.gif" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJu6YuJQNJCSnrDHqvpszfnLOJPGUyhxfIXmXrySiHnnWQDlwENVQE70VN2Kjz0IX6QNPXIUTY3fqSQ0xFJbnBhNFOP-d0CbIFG8jcBzXlkh2QWvHUF2aROLCDr4285eqOeeh4/s200/highlyaccessed.gif" border="0" alt="" id="BLOGGER_PHOTO_ID_5616566088708123026" style="cursor: pointer; width: 91px; height: 12px; " /></a> Hughes, J. (2011). TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics 12: 178 doi: <a href="http://dx.doi.org/10.1186/1471-2105-12-178">10.1186/1471-2105-12-178</a></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-19800746953249785262011-05-20T14:05:00.005+00:002011-05-20T14:20:41.572+00:00Insect systematics: you've got to laugh, if you didn't you'd cry<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUTQknikfKqEEhHbTnPJV9x_5acIprbnXd9eM0ay08M2V-k5V0601fki9lBJPw8oU6hL9bLapIsWACJJZSqLovexjsOdx_yjv1049yuaW6PcTbENtJZV4GfmswUwGOS3ivMDf7/s1600/All.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 390px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUTQknikfKqEEhHbTnPJV9x_5acIprbnXd9eM0ay08M2V-k5V0601fki9lBJPw8oU6hL9bLapIsWACJJZSqLovexjsOdx_yjv1049yuaW6PcTbENtJZV4GfmswUwGOS3ivMDf7/s400/All.jpg" alt="" id="BLOGGER_PHOTO_ID_5608801143460094578" border="0" /></a><br /><br />In continuation from my <a href="http://evo-karma.blogspot.com/2011/05/many-outstanding-questions-in.html">previous post</a>, I have now assembled 43 order level phylogenies of insects, i.e. they are based on more or less independent sources of data. The oldest study included is from 1993, so I still have my work cut out to find trees published before then especially as it becomes increasingly hard to get your hands on the articles as you go further back in time.<br />As more phylogenies are included, it also becomes hard to visualize this increasingly complex network on a 2D screen and I which I could explore it in a more intuitive way.<br /><br /> <div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=6860b281-9e74-46bc-8f5a-0fa97ff07343" alt="Enhanced by Zemanta" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-27495650775813242232011-05-04T11:35:00.003+00:002011-05-04T12:01:38.112+00:00Many outstanding questions in the phylogenetic relationships of insect orders<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWZobYfUIOp02XxO5x-1l_5HHS8PZV2graD-Db9GllFbzNDa49DBz3TYD5aC-laRW8RoplTIc2I92miWfng_wjgvAcIbBGVwKGlFQAOwcs61O-bkn_CsElMqG9rx54V-nL-MLa/s1600/AllTrees.trees_cpy4.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 400px; height: 311px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWZobYfUIOp02XxO5x-1l_5HHS8PZV2graD-Db9GllFbzNDa49DBz3TYD5aC-laRW8RoplTIc2I92miWfng_wjgvAcIbBGVwKGlFQAOwcs61O-bkn_CsElMqG9rx54V-nL-MLa/s400/AllTrees.trees_cpy4.jpg" alt="" id="BLOGGER_PHOTO_ID_5602824275662422178" border="0" /></a>I am trying to get my head around the multiplicity of phylogenetic hypotheses for insect phylogenetic relationships in continuation from my previous <a href="http://evo-karma.blogspot.com/2010/11/comparing-different-hypotheses-for.html">post</a>. I have been gathering a number of insect phylogenies from the literature (these include morphological and molecular based phylogenies). I wanted to illustrate where the hypotheses were conflicting so I used a SuperNetwork with no edge weights in <a href="http://www.splitstree.org/">SplitsTree</a>. This gives an idea of how much conflicting evidence there still is at the base of the Pterygota and also the large number of studies that have focused on the Endopterygota, in particular the relationship of the Strepsiptera to the other orders. Many of the orders have only been included in one study, in particular the basal orders. What I would like to do at some point, is show how the insect phylogeny has changed over time by layering the phylogenies chronologically onto one another to form the above SuperNetwork.<br /><br /> <div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=d8a86295-ce12-405e-8250-b3a508e3b48b" alt="Enhanced by Zemanta" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com2tag:blogger.com,1999:blog-22250336.post-20808839088404170922010-11-05T16:35:00.007+00:002010-11-05T16:50:53.712+00:00Comparing the different hypotheses for Strepsiptera<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyug7emggg5LXylGfgwZFM9k4_7Xd6ToLOSxpq9Ykzght7jrPOe80IpB0jfo3np5LStM-pwg0jMwP4G7W7rAvQYdQDhCCLYL7uRXIzdvlq9lCdK9zWKKJEMqVuNbeKbFx58izt/s1600/MetatreeScreenshot.png"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 320px; height: 234px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyug7emggg5LXylGfgwZFM9k4_7Xd6ToLOSxpq9Ykzght7jrPOe80IpB0jfo3np5LStM-pwg0jMwP4G7W7rAvQYdQDhCCLYL7uRXIzdvlq9lCdK9zWKKJEMqVuNbeKbFx58izt/s320/MetatreeScreenshot.png" alt="" id="BLOGGER_PHOTO_ID_5536106131863432482" border="0" /></a><span class="zemanta-img separator" style="clear: right;"><a href="http://commons.wikipedia.org/wiki/File:Strepsiptera-halictophagida.gif" style="margin-left: 1em; margin-right: 1em; display: block; float: right; clear: right;"><img src="http://upload.wikimedia.org/wikipedia/commons/thumb/7/72/Strepsiptera-halictophagida.gif/300px-Strepsiptera-halictophagida.gif" alt="Halictophagidae" style="font-size: 0.8em; border: medium none;" height="234" width="300" /></a><span class="zemanta-img-attribution" style="margin-left: 1em; margin-right: 1em; clear: both; float: right; width: 300px;">Image via <a href="http://commons.wikipedia.org/wiki/File:Strepsiptera-halictophagida.gif">Wikipedia</a></span></span><br />I have been comparing the different phylogenetic hypotheses for the Strepsiptera. As always, it has been hell to get the trees from images back into a suitable format for topology comparison. I have used the program <a href="http://www.mas.ncl.ac.uk/%7Entmwn/phylo_comparison/multiple.html">METATREE</a> for comparing multiple trees. The tree of trees essentially shows the two main hypotheses "Strepsiptera sister to Diptera" supported by the studies of Whiting and Wheeler using 18S and 28S rDNA, and at the other end of the metatree the "Strepsiptera sister to Coleoptera" supported by morphological studies and recent molecular studies using nuclear genes. Other differences in the Holometabola topologies are also illustrated in the metatree such as the variable position of the Hymenoptera. Anyway, to me, it looks like the research community is reaching a consensus on the "Strepsiptera problem": Strepsiptera sister to Coleoptera. What do you think? <div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=3317fbec-fb3d-4784-87d1-9ac65083638e" alt="Enhanced by Zemanta" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com4tag:blogger.com,1999:blog-22250336.post-77558259193983189092010-10-15T19:59:00.004+00:002010-10-15T20:07:17.790+00:00TreeRipper: towards a fully automated optical tree recognition softwareUnfortunately my TreeRipper program has been rejected from BMC bioinformatics for now because there are too many delegate programs that the reviewers didn't manage to install successfully. So until I manage to find time to make a makefile that can deal with the installation on multiple platforms, I have put the manuscript on <a href="http://dx.doi.org/10.1038/npre.2010.4997.1">Nature precedings</a> and you can find the code at <a href="http://code.google.com/p/treeripper/">google code</a>. I think I am the first to attempt to fully automate the conversion of a tree image into something more useful for researchers and I hope that what I have done can be built upon and improved. I have attached to the code a set of images and tree files that might be useful for training and/or benchmarking future programs.<br /><div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=ca25d5cd-d17c-4184-8f79-8ca927cb3950" alt="Enhanced by Zemanta" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-44198614936328612212010-09-01T08:49:00.005+00:002010-09-03T12:12:38.881+00:002nd UK RAD Sequencing Meeting: wrap-up #RADseq<span class="zemanta-img separator" style="clear: right;"><a href="http://commons.wikipedia.org/wiki/File:ThreeSpinedandTenspinedSticklebackMales.JPG" style="margin-left: 1em; margin-right: 1em; display: block; float: right; clear: right;"><img src="http://upload.wikimedia.org/wikipedia/commons/thumb/8/82/ThreeSpinedandTenspinedSticklebackMales.JPG/300px-ThreeSpinedandTenspinedSticklebackMales.JPG" alt="Males in breeding colors of the three spined s..." style="font-size: 0.8em; border: medium none;" height="224" width="300" /></a><span class="zemanta-img-attribution" style="margin-left: 1em; margin-right: 1em; clear: both; float: right; width: 300px;">Image via <a href="http://commons.wikipedia.org/wiki/File:ThreeSpinedandTenspinedSticklebackMales.JPG">Wikipedia</a></span></span>The 2nd UK RAD sequencing meeting took place at the e-Science institute in Edinburgh. John Davey did a brilliant job of organizing the event and the e-Science is always a good venue for meetings and workshops.<br />The meeting was split into the morning session were we heard from the developers of RAD-sequencing and useful bioinformatic tools from John Davey: <a href="https://www.wiki.ed.ac.uk/display/RADSequencing/Home">RADtools</a>.<br />Dr William Cresko (Oregon) talked about the history of RAD tags and some recent applications in <a href="http://creskolab.uoregon.edu/">their lab</a> which mainly center around understanding phenotypic evolution in the non-model three spined stickleback.<br />Dr Susan Bassham (Oregon) brought up quite a few practical issues on the molecular side of things. One that stuck to mind, is that it is much better to use restriction enzymes that will result in similar fragment sizes and smaller fragments are better so that the intensity of the dots on the Illumina cell are similar. Ideally, the GC content of your samples that you are planning to mix, should have similar GC-content, so mixing different species is probably not recommended.<br /><br />Dr Paul Hohenlohe (Oregon) talked about cleaning up the data after sequencing. How to detect sampling biases: different tags, different alleles and sequencing errors. Other sources of error include PCR variance, polymorphisms at the RAD sites. All these need to be accounted for in the analyses. He has developed a maximum likelihood genotyping based on multinomial distribution of the reads. The sequencing error parameter is estimated independently for each site. His <a href="http://www.blogger.com/www.pnas.org/cgi/doi/10.1073/pnas.1006538107">most recent paper</a> goes into further detail.<br /><br />Dr Simon Baxter (Cambridge) is using RAD-tags for gene discovery and linkage mapping in the Diamond-back moth. He is mainly interested in the evolution of resistance to pesticides.<br /><br />Dr Maureen Liu (Nottingham) is using RAD-tag to determine the genetic mechanism for Left-Right chirality in the pond snail. Out of the 70,000 RAD-tags she got from cutting the 1.4Gb genome with the restriction enzyme SbfI, she found a subset of 19 that were linked to chirality. She also managed to link it to a specific gene but kept the name of the gene hush hush.<br /><br />Dr Shapiro and Dr Justin Gerke (Princeton) used RAD-tag for a global survey of <span style="font-style: italic;">C. elegans</span>. They found that some strains share nothing, others share everything but most share about 40% of their genome and 94% of the strain pairs analysed share one fragment. The fragments shared are also large. They suggest that this may be due to recent migration but selection, both background selection and positive sweep, may also play a role.<br /><br />The remaining afternoon talks were about projects that were getting started and it was a good opportunity for the speakers to receive advice from the guys who had already used RAD-tag.<br /><ul><li>Developing RAD markers as a resource for plant breeding using the perennial ryegrass Lolium perenne. Dr Matt Hegarty (Aberystwyth)<br /></li></ul><ul><li>Unearthing the functionally relevant genetic diversity from the earthworm<br />genome. Dr Pete Kille (Cardiff)<br /></li><li>Exploring the use of RAD markers in tree breeding programmes. Dr Pablo Fuentes Utrilla (Edinburgh)<br /></li><li>RAD Sequencing for applied conservation genetics. Dr Rob Ogden (TRACE Network, Edinburgh)<br /></li><li>Adaptive significance and genetic basis of a balanced colour-<br />polymorphism in Philaenus spumarius. Dr Octavio Paulo (Lisbon)<br /></li><li>RAD genetic mapping of reproductive mode in tadpole shrimps. Tom Mathers (Hull)<br /></li><li>The genetic architecture of a fundamental social trait. Dr Yannick Wurm (Lausanne)<br /><br /></li></ul>All the talks were very honest about the difficulties of the approach. I really got the feeling that the community was working together to improve the technique and advise researchers on how to use the method.<br /><br /><span style="font-weight: bold;">Update: </span>The talks are now available <a href="http://www.nesc.ac.uk/action/esi/contribution.cfm?Title=1090">here</a>.<br /><div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=0d38ef87-a14b-4a2b-a19a-0b10f572ed21" alt="Enhanced by Zemanta" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-13221622159244925372010-08-26T10:51:00.007+00:002010-08-26T14:01:31.002+00:00Google Voice, Skype or TalkTalk<span class="zemanta-img separator" style="clear: right;"><a href="http://commons.wikipedia.org/wiki/File:1881-1899_Bandera_de_M%C3%A9xico.JPG" style="margin-left: 1em; margin-right: 1em; display: block; float: right; clear: right;"><img src="http://upload.wikimedia.org/wikipedia/commons/thumb/a/a7/1881-1899_Bandera_de_M%C3%A9xico.JPG/300px-1881-1899_Bandera_de_M%C3%A9xico.JPG" alt="Mexican Flag in the 19th century" style="font-size: 0.8em; border: medium none;" width="300" height="200" /></a><span class="zemanta-img-attribution" style="margin-left: 1em; margin-right: 1em; clear: both; float: right; width: 300px;">Image via <a href="http://commons.wikipedia.org/wiki/File:1881-1899_Bandera_de_M%C3%A9xico.JPG">Wikipedia</a></span></span>This morning, when I logged into my Google account, I got a little pop-up ad saying that I had $0.1 Google Voice credit. Prices seem cheap and I want to see whether it will be worth me using GoogleVoice instead of Skype for my calls. I have already posted a comparison of VoipCheap, Skype and Gizmo <a href="http://evo-karma.blogspot.com/2006/04/switching-to-gizmo-is-it-worth-it.html">here</a>. It looks like Google have set themselves up in direct competition with Skype so I am going to try to work out when I would be better off using GoogleVoice.<br />We tend to call friends and family in Mexico, France, Norway and occasionally Spain.<table summary="This table gives some statistics call prices for various Voice Over IP providers" border="1"><br /><caption><em>Prices in pence per min incl. VAT</em></caption><br /><tbody><tr><th>Table<br /></th><td>GoogleVoice<br /></td><td>SkypeOut*<br /></td></tr><br /><tr><th>Mexico (Landline)</th><td>6.5</td><td>6.4</td></tr><br /><tr><th>Mexico (Mobile)</th><td>12</td><td>20.7</td></tr><br /><tr><th>Mexico-Guadalajara (Landline)</th><td>1.3</td><td>2.1</td></tr><br /><tr><th>Mexico-Mexico City (Landline)</th><td>1.3</td><td>1.4</td></tr><br /><tr><th>Mexico-Mexico City (Mobile)</th><td>12 ?</td><td>20.7 ?</td></tr><br /><tr><th>Mexico-Monterrey (Landline)</th><td>1.3</td><td>1.4</td></tr><br /><tr><th>France (Landline)</th><td>1.3</td><td>1.4<br /></td></tr><br /><tr><th>France (Mobile)</th><td>9.7</td><td>13.2</td></tr><br /><tr><th>norway (Landline)</th><td>1.3</td><td>1.4</td></tr><br /><tr><th>norway (Mobile)</th><td>13</td><td>13.8</td></tr><br /><tr><th>spain (Landline)</th><td>1.3</td><td>1.4</td></tr><br /><tr><th>spain (Mobile)</th><td>12</td><td>17.7</td></tr></tbody></table><br />There's very little in it when comparing calls to landlines but Google Voice does seem to be cheaper when calling mobiles. I will check sound quality but unless it is way better than Skype, I will stick with the devil I know.<br /> <div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=a606facc-d142-4ca0-9667-6c82c5df629d" alt="Enhanced by Zemanta" /></a></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com2tag:blogger.com,1999:blog-22250336.post-35122398946801538902010-08-06T15:34:00.004+00:002010-08-06T15:46:51.801+00:00Getting Evernote to OCR for you<a class="zem_slink" href="http://www.evernote.com/" title="Evernote" rel="homepage">Evernote</a> is a great app that lets you make notes, take photos and screenshots, bookmark webpage and syncs everything so that you can access it from any computer, iphone or ipad. What I love about it, is that when you take a screen shot, it uploads the image to its server and tries to OCR the text, even hand-written text. Although technically speaking, Evernote doesn't actually do OCR:<br /><span style="font-size:78%;"><span style="font-style: italic;">"Evernote's image processing technology is a bit different. We analyze the image to generate a set of possibilities for each word that we see in an image. Each possible interpretation is given a score.</span><br /><span style="font-style: italic;">For example, we may look at a word and decide that this word may either be "clue" or "due", and we can assign a score to each possibility. This set of scored possibilities is stored in our database for searching.</span><br /><br /><span style="font-style: italic;">As a result, there isn't a simple text representation that you can use. Instead, you can search our database to find the image based on the different sets of possible interpretations for each word."</span><br /><br /></span>Well, there is a way to get to that OCRed text (or data interpretation). You can find it in the files in Metadata/com.evernote.Evernote. Just in case anybody was wondering.<br /><div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://www.zemanta.com/" title="Enhanced by Zemanta"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/zemified_e.png?x-id=6ded9d1e-9992-4196-aebb-8ab9fd0f6d0e" alt="Enhanced by Zemanta" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com2tag:blogger.com,1999:blog-22250336.post-91955623169754109452010-06-03T11:01:00.005+00:002010-07-17T13:24:52.742+00:00The long short communication of M. Stift<a href="http://sites.google.com/site/marcstift/">Marc Stift</a> also know as Stifty by some, has recently left Glasgow for the sunnier climate of Portugal. Just this week, the (not so short) <a href="http://dx.doi.org/10.1111/j.1420-9101.2010.02012.x">short communication</a> that he worked on tirelessly, has been published. I kept on trying to convince him that it was important that people understood the statistics of small sample size and that he should include the simulation graphs that he generated for determining the statistical power when determining the inheritance in tetraploids (but he ignored me). This is probably for the best as the figures would probably just have lingered in the depths of the supplementary materials. I am still working on convincing him to release those figures which might end up in his first blog or in a second paper. I'll keep you informed!blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com3tag:blogger.com,1999:blog-22250336.post-60662031201491637752010-05-31T08:57:00.006+00:002010-05-31T10:08:54.906+00:00Increasingly wondering what publishers do for science and researchIt seems that researchers are increasingly using Open Acesss (<a class="zem_slink" href="http://en.wikipedia.org/wiki/Open_access_%28publishing%29" title="Open access (publishing)" rel="wikipedia">OA</a>) platforms like <a href="http://arxiv.org/">Arxiv</a> or<a href="http://arxiv.org/"> Nature Precedings</a> to disseminate their work. Authors often submit their pre-print manuscript version to these sites or to in-house depositories, for example <a href="http://eprints.gla.ac.uk/">Enlighten</a> at the University of Glasgow. Researchers are at least encouraged to do this by funding bodies and research institutions.<br />This often means that the article is in circulation before the publisher's nicely formatted version (see for example, Rod's <a href="http://iphylo.blogspot.com/2010/04/elsevier-grand-challenge-paper-out.html">Elsevier Grand Challenge Paper</a>) and begs the question "What do the publishers do for research and the scientific process?".<br />Ten years ago, it was easy to see the role that publishers had, they disseminated your work by convincing libraries and individuals to subscribe to their journals. In this way, your research had a chance to be seen on a few library shelves across the world after a few months of format checking and page layout with the publisher. But now, the worldwide web does that for you and does it immediately!<br />O.K., publishers do play an important role in the review process. They make sure they get a famous and qualified editorial board who select good papers for review and choose good reviewers for the job. This increases the impact of the journal and so feeds back into the status of the journal and the publishers. But increasingly, this seems to be the only thing that publishers are providing and could be done by other institutions like universities.<br />It seems that publishers have caught onto the fact that things are changing fast and they need to do something about it. One solution is to enrich the readers experience of a paper if he reads it on the publishers website as opposed to the pre-print pdf version in these OA archives. This, I think, was the idea behind the <a href="http://www.elseviergrandchallenge.com/index.html">Elsevier Grand Challenge</a> and perhaps behind the <a href="http://everyone.plos.org/2010/05/24/announcing-the-plos-hub-for-biodiversity-call-for-articles/">PLoS Hub for Biodiversity</a> . There is no doubt that we are in need of better ways of finding research and data with <a href="http://www.mendeley.com/blog/design-research-tools/what%E2%80%99s-relevant-to-me-right-now/">the ever increasing number of publications to keep up with</a>.blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-82114906031389264082010-04-21T12:29:00.004+00:002010-04-26T10:25:16.418+00:00A way to improve the commenting system on publicationsI was chatting to <a href="http://iphylo.blogspot.com/">Rod</a> a few days ago about his visit to CalAcademy for a <a href="http://twitter.com/search?q=%23plosmarkup">Plos markup meeting</a> and our disucssion strayed onto the commenting system of publications like <a href="http://www.plos.org/">Plos</a> and the <a href="http://www.biomedcentral.com/">Biomed Central Journals</a>. I was saying to him that I had left a few comments both as an individual and as a member of the molecular ecology discussion group in the department (not that I can remember the journal or the narture of the comments anymore) and that I had never received a response or feedback from the authors of the manuscript. Additionally, it isn't possible for me to get a list of the comments that I have left. Rod suggested that really what these sites needed was a way<br />to credit readers and commentors of the articles in a similar way to <a href="http://disqus.com/">Disqus</a>. Disqus is great, because all the comments you make on a range of different blogs and sites can all be accessed at Disqus, you can manage them yourself, edit them and delete them. You are in control of what<br />you have written. You can also see all the responses to your comments. Additionally, you get credits from fellow commentors for the comments and ideas that you put forward. It would be great if you could have the same level of control over the comments you leave on manuscripts at Plos and Biomed Central.<br />So I wrote a quick email to the guys over at Biomed Central:<br /><br /><span style="color: rgb(102, 102, 102);">Hi,</span><br /><span style="color: rgb(102, 102, 102);">I was wondering whether there was a central page I could go to, </span><br /><span style="color: rgb(102, 102, 102);">to see the comments I have left on manuscripts along with the responses to </span><br /><span style="color: rgb(102, 102, 102);">those comments. If this doesn't exist, I think it should. Creating a system </span><br /><span style="color: rgb(102, 102, 102);">of commenting like disqus might encourage more people to comment on articles. </span><br /><span style="color: rgb(102, 102, 102);">It enables the commentor to keep track of their comments, receive feedback, get rated and thus gives an incentive to comment. You could just enable disqus on your site.</span><br /><br /><span style="color: rgb(102, 102, 102);">Kind regards,</span><br /><span style="color: rgb(102, 102, 102);">Joseph Hughes</span><br /><br /><br />I got this in reply:<br /><br /><span style="color: rgb(102, 102, 102);"> Dear Joseph Hughes</span><br /><span style="color: rgb(102, 102, 102);">Thank you for contacting BioMed Central.</span><br /><span style="color: rgb(102, 102, 102);">Readers' Comments are available to view on the right-hand menu of all published articles:</span><br /><span style="color: rgb(102, 102, 102);">The link below will take you to an example article where a comment has been left, you can access the article by clicking the associated link in the right-hand menu:</span><br /><span style="color: rgb(102, 102, 102);">http://www.biomedcentral.com/1471-2105/10/2</span><br /><span style="color: rgb(102, 102, 102);">If you have any questions please don't hesitate to contact me.</span><br /><br /><span style="color: rgb(102, 102, 102);">Best wishes </span><br /><span style="color: rgb(102, 102, 102);">David Roman </span><br /><br /><br />Either I was unclear or they just don't get it! In any case, I am very pessimistic about the system of commenting getting any better in the near future.<br /><br /> <div style="margin-top: 10px; height: 15px;" class="zemanta-pixie"><a class="zemanta-pixie-a" href="http://reblog.zemanta.com/zemified/6c8ec23c-76ef-48b8-b231-7242e8d1ca12/" title="Reblog this post [with Zemanta]"><img style="border: medium none; float: right;" class="zemanta-pixie-img" src="http://img.zemanta.com/reblog_e.png?x-id=6c8ec23c-76ef-48b8-b231-7242e8d1ca12" alt="Reblog this post [with Zemanta]" /></a><span class="zem-script more-related pretty-attribution"><script type="text/javascript" src="http://static.zemanta.com/readside/loader.js" defer="defer"></script></span></div>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com4tag:blogger.com,1999:blog-22250336.post-1151185328567105462010-02-05T14:36:00.004+00:002010-02-05T15:39:09.989+00:00The people behind the paperI thought it might be interesting for readers to hear about how our recent paper came together and especially who the people are behind the names. A while back, samples of <font style="font-style: italic;">Halipeurus</font> lice landed on Rod Page's desk. As a postdoc in his lab, I was charged with storing them in the freezer and entering the relevant data in the now defunct lousebase, although the data is now available on Google Docs. <br /><a href="http://www.zsl.org/science/ioz-staff-students/brown,1112,AR.html">Ruth Brown</a>, a PhD student at the time working at the Zoological Institute London, had sent the samples, suggesting that it would be interesting to sequence them. The specimen came from the Trindade petrel (<font style="font-style: italic;">Pterodroma arminjoniana</font>) on Round Island (near Mauritius) where she had been working for her thesis. The presence of this petrel on Round Island was probably a recent colonisation as there were no records of the petrel on the island prior to the 1960s.<br />I did not realize why it would be interesting to do this sequencing until I met Leandro Bugoni from Brazil. He was just finishing his PhD at the University of Glasgow with Bob Furness. He had been working on the Trindade petrel on Trindade Island (near Brazil). Interestingly, they had found little difference between these two island bird populations whether it was based on genetic markers, morphology or calls and yet they hosted different lice species.<br />We knew this thanks to the expert identification skills of <a href="http://www.phthiraptera.org/Phthirapterists/palma/palma.htm">Ricardo Palma</a> based at the <a href="http://www.tepapa.govt.nz/pages/default.aspx">Museum of New Zealand Te Papa Tongarewa</a> and whom I had collaborated with before on <span style="font-style:italic;">Pectinopygus</span> lice on pelicans.<br />What we did not know, was how these two lice species were related, how divergent they were and their origin. Had they always been associated with the Trindade Petrel? Had they recently parasitized one of the bird populations?<br />Fortunately, a friendly Faroese MRes student, Sjudur Hammer, chose my suggested project proposal and did all the lab work. He copped very well in the lab and managed to get some good quality sequences for the <span style="font-style: italic;">Halipeurus</span> lice from both islands.<br />And voila! We published what I think is a cool <a href="http://dx.doi.org/10.1016/j.ympev.2010.01.013">cospeciation study of lice and gadfly petrels</a> and it was a pleasure to collaborate with such an international group of researchers.blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-50494772597124998222010-02-04T12:29:00.005+00:002010-02-04T12:53:22.452+00:00Image searchingI have been trying to find images on the web that will match images that I upload and I have come across a few cool websites.<br />To start with there is <a href="http://pixolu.does-it.net/#">pixolu</a>. Although it doesn't enable you to upload an image, it lets you search for particular key words and then select the types of images that you would like. <a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSk3x7xh_X4yOB1eoaRGlWPrRqZsm-6e1xyYfB6ZnSeC9f1gyZRIE4bc7q021-DqhAzuRyvSLdKGnJe0hafR785glZIBDacS4iabOpnt4qhCWWbOAeT5OrBbgUz85vWQ_1ck88/s1600-h/Picture+3.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 179px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSk3x7xh_X4yOB1eoaRGlWPrRqZsm-6e1xyYfB6ZnSeC9f1gyZRIE4bc7q021-DqhAzuRyvSLdKGnJe0hafR785glZIBDacS4iabOpnt4qhCWWbOAeT5OrBbgUz85vWQ_1ck88/s320/Picture+3.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5434370397949959074" /></a>Using these images, it then refines the search to find images similar to those that you have selected. I thought it was a very nifty tool. This is quite similar to <a href="http://similar-images.googlelabs.com/">Google Similar Image</a>, except that it has a nicer interface and a lot of images in the Google Similar don't actually have a similar even though the same image in pixolu does.<br />Then there is <a href="http://labs.systemone.at/retrievr">retrievr</a> which still doesn't let you upload an image but you can squiggle something in a box an it will find similar images on the web. I was impressed to find that when I did a very rough drawing of a tulip, the search did pull up an image of a tulip (see the screenshot).<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlEneV7gCWJ7CUOscrxkRMyZtEh_vlIQBcDgojTGgpBwL5RB7gRjRstzBLnsHTphrzJ_VMNLv7oinNZxHlFKimAp4u_b4DwXggUA-QcccLYvT5zDnljy7TAY7_kJmTIkogX5Zj/s1600-h/Picture+1.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 214px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlEneV7gCWJ7CUOscrxkRMyZtEh_vlIQBcDgojTGgpBwL5RB7gRjRstzBLnsHTphrzJ_VMNLv7oinNZxHlFKimAp4u_b4DwXggUA-QcccLYvT5zDnljy7TAY7_kJmTIkogX5Zj/s320/Picture+1.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5434366547120603170" /></a><br />But something like <a href="http://www.gazopa.com/">Gazopa</a> was what I was really looking for. Unfortunately, it doesn't work as well as I would hope. Even though the image I upload is available on Flickr, it doesn't actually find it. It does do a good job at finding images with similar colours (see screenshot).<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgN74z6DEuOaJzI3MZvyAT0rI1Ehd1JTNfbT4FYauHpjHY0wQRXN5OW9r6geUBkF6LLnBsJS9PUbvlefbDfHUoC4qhOyR9aUXtYtBVBSe6Dpni5hJzSmP9UAXk5fhFpL7KEXrei/s1600-h/Picture+2.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 320px; height: 166px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgN74z6DEuOaJzI3MZvyAT0rI1Ehd1JTNfbT4FYauHpjHY0wQRXN5OW9r6geUBkF6LLnBsJS9PUbvlefbDfHUoC4qhOyR9aUXtYtBVBSe6Dpni5hJzSmP9UAXk5fhFpL7KEXrei/s320/Picture+2.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5434369542322259058" /></a>blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-44214782986231261142010-01-14T10:26:00.005+00:002010-01-14T11:35:48.761+00:00Species Image ReCAPTCHAAfter seeing the inspiring talk of <a href="http://www.poptech.org/blog/video_luis_von_ahn_harnesses_brainpower.html">Luis von Ahn</a> on PopTech, I was thinking that CAPTCHA (Completely Automated Public Turing test to tell Computers and Humans Apart) could be a cool way to improve the OCR of species names in books OCRed by the <a href="http://www.biodiversitylibrary.org/">Biodiversity Heritage Library</a> particularly as <a href="http://www.blogger.com/profile/00269598293846172649">Rod</a> is currently using ReCAPTCHA on <a href="http://biostor.org/">BioStor</a>. BioStor is helping to annotate and extract data from BHL and Rod is using ReCAPTCHA to check that the annotation is being made by a human. <br />In my limited experience of OCRing, I have found that italicized species names are particularly hard to get right, so if ReCAPTCHA could be set-up to to use species names from BHL, then users annotating BioStor would be improving the OCRing of BHL articles and helping to annotate it.<br />Along the same lines, I have been thinking that it would be great if you could use the power of the brain to annotate species images that are on the web, a bit in the style of Google's <a href="http://images.google.com/imagelabeler/">Image Labeler</a> which I find addictive so have been avoiding it for a while. Then quite by chance, I came across this image CAPTCHA at the University of Edinburgh. <a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJInBiF1f_SgY_lH7p1pzdnFX5rSVvbRzvVmy5V455BUF6AZU-WqUioVFVZ7sjcq0WoBeYvqEwbxZXhcSL0B_hqauqyKLOlNH800HlUIO00fAhYE6eviX6Wyp91w4UzhLdUNY0/s1600-h/Picture+1.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 118px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJInBiF1f_SgY_lH7p1pzdnFX5rSVvbRzvVmy5V455BUF6AZU-WqUioVFVZ7sjcq0WoBeYvqEwbxZXhcSL0B_hqauqyKLOlNH800HlUIO00fAhYE6eviX6Wyp91w4UzhLdUNY0/s400/Picture+1.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5426555619939890770" /></a><br />I thought this would be a really cool way to help tag wildlife images at least using common names. You could also do a pro version for taxonomists with latin binomial tagging.blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com0tag:blogger.com,1999:blog-22250336.post-61410066768592060452009-12-24T12:08:00.001+00:002009-12-24T12:10:57.074+00:00The facts about bottled waterPresented by <a href="http://www.onlineeducation.net">Online Education</a><br><a href="http://www.onlineeducation.net/bottled_water/"><img src="http://www.onlineeducation.net/bottled_water/water_full.jpg" alt="The Facts About Bottled Water" width="450" border="0" /></a><br />blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com1tag:blogger.com,1999:blog-22250336.post-1130517064813872222009-12-09T09:58:00.005+00:002009-12-09T10:25:14.463+00:00Motion Chart of NCBI data<script src="https://spreadsheets.google.com/gpub?url=http%3A%2F%2Foj0ijfii34kccq3ioto7mdspc7r2s7o9.spreadsheets.gmodules.com%2Fgadgets%2Fifr%3Fup__table_query_url%3Dhttps%253A%252F%252Fspreadsheets.google.com%252Ftq%253Frange%253DA1%25253AI71%2526headers%253D-1%2526gid%253D1%2526key%253D0AiSgKa0NqxSNdGx1M0xvRkdpT2ZVckR6b2wtTTJGeHc%2526pub%253D1%26up_title%3DCumulative%2520NCBI%2520data%26up_initialstate%3D%26up__table_query_refresh_interval%3D300%26url%3Dhttp%253A%252F%252Fwww.google.com%252Fig%252Fmodules%252Fmotionchart.xml&width=450"></script><br />The last decade has seen a huge increase in sequence data in public databases with an impressive increase in species coverage. Here, I have used Google's Motion Chart API and Google spreadsheet do illustrate the changes in numbers of sequences and numbers of species for <a href="http://www.ncbi.nlm/Taxonomy/taxonomyhome.html">different taxonomic groups</a>. Whilst the nucleotide sequence increase against the number of species sequenced has been exponential for all taxonomic groups, the rate of increase in nucleotide sequences per species appears to have accelerated since 2007 for Fungi and Bacteria. The gap also seems to be widening between the number of nucleotides per species in the Metazoa compared the Viridiplantae. There appears to be no signs of a plateau and with the next-generation sequencers, we are likely to soon see an even sharper increase in the number of nucleotides per species. However, I suspect the rate at which additional species are added to NCBI might begin to slow as we find it harder to collect and sample novel species.blOghttp://www.blogger.com/profile/16883530682517464163noreply@blogger.com2