Notes from the Biomass (A Bioinformatics Blog)
http://binf.twoday.net/
A Bioinformatics Blog
spitshine
spitshine
2006-07-16T11:11:56Z
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2000-01-01T00:00:00Z
Notes from the Biomass
http://static.twoday.net/binf/images/icon.jpg
http://binf.twoday.net/
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Last post
http://binf.twoday.net/stories/2357166/
Notes from the biomass will continue at <a href="http://nftb.net">nftb.net</a>.<br />
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My thanks to twoday.net, their service is recommended for everyone who is just starting to blog and doesn't want to be bogged down by administration of their own blog. However, at this point I need to move on and make use of more advanced software, most notably <a href="http://structuredblogging.com">structured blogging</a>.
spitshine
<a href="http://binf.twoday.net/topics/Meta">Meta</a>
Copyright © 2006 spitshine
2006-07-16T10:56:00Z
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Latter posts - comment spam
http://binf.twoday.net/stories/1894164/
Things to do when you're not blogging: Taking care of comment spam. After I revisited this site recently, I had questionable fun with several comments in German. They were just statements of admiration by Gotfrid and Hans and other namesakes of baddies from <i>Die Harder Than You Can Possibly Imagine Reloaded</i>, written within ten minutes. Still, there was a little lag time before I realized that they truly were spam and at first, I felt hurt. I do write in my second language,...
spitshine
<a href="http://binf.twoday.net/topics/Blogs">Blogs</a>
Copyright © 2006 spitshine
2006-04-29T16:45:00Z
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Latter posts - further reading
http://binf.twoday.net/stories/1785291/
Why don't you turn to a book, read a comic or scientific paper? Some all time favourites that crossed my path recently.
<p>
<h4>A 120 page novel</h4>
Stanislaw Lem, one of my favorite authors died recently. As his best story (Experimenta Felicitologica) is not available in English - well read the <a href="http://www.sfsite.com/~silverag/lem.html">Futurological Congress</a>. Still excellent after the 5th time.
<p>
<h4>Evolutionists are the...
spitshine
<a href="http://binf.twoday.net/topics/Blogs">Blogs</a>
Copyright © 2006 spitshine
2006-04-03T17:34:40Z
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Latter posts - Part 1
http://binf.twoday.net/stories/1765334/
365 days ago I started to blog about life sciences and bioinformatics in this spot - for one year. The experiment is over and I might review what has happened in the next couple of days in more details. However, I have decided to discontinue Notes from the Biomass in its current form.<br />
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A blog break hopefully gives me the opportunity to reconsider many things. Blogging takes time. It depends on your perception of the day whether it takes too much of it. I became pretty blog...
spitshine
<a href="http://binf.twoday.net/topics/Blogs">Blogs</a>
Copyright © 2006 spitshine
2006-03-29T19:51:04Z
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Hard blogging scientists at work
http://binf.twoday.net/stories/1731497/
The keywords <a href="http://www.technorati.com/blogs/biology">Biology</a> or <a href="http://www.technorati.com/blogs/science">Science</a> in Technorati are dominated by popular science blogs, many of them discussing other topics ranging from politics to Harry Potter side by side. My preferences for this blog are different: I concentrate on sciene - bioinformatics and genomics - and mainly want to communicate with fellow scientists on special interest...
spitshine
<a href="http://binf.twoday.net/topics/Blogs">Blogs</a>
Copyright © 2006 spitshine
2006-03-22T13:53:35Z
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Alone down there
http://binf.twoday.net/stories/1702480/
Today, the Daily Transcript (a recent scienceblogs addition) lists the <a href="http://scienceblogs.com/transcript/2006/03/the_worst_parts_of_scientific.php">worst parts</a> of scientific life. Somehow I cannot tune in the crying tonight - being a scientist of the best jobs I can think of on this planet. However, if your gel was empty, you can't find the bug in your own 3 lines of code and your arch-nemesis just published your good idea with sloppy and inconclusive data...
spitshine
<a href="http://binf.twoday.net/topics/Blogs">Blogs</a>
Copyright © 2006 spitshine
2006-03-15T17:30:43Z
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Accessing sequence information by location
http://binf.twoday.net/stories/1696770/
The three major DNA sequence repositories (Genbank, EMBL, and DDBJ) decided to include for a <a href="http://www.insdc.org/feature_table.html">location identifier</a> in 2005. You can now access EMBL via <A href="http://www3.ebi.ac.uk/Services/EMBLWorld/EMBLWorld.html">a map of the world</a>. <br />
<img width="400" height="150" title="" src="http://static.twoday.net/binf/images/sevorld.png" alt="sevorld"...
spitshine
<a href="http://binf.twoday.net/topics/Useful+tools">Useful tools</a>
Copyright © 2006 spitshine
2006-03-14T16:38:51Z
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Scientific open source software
http://binf.twoday.net/stories/1688996/
The market for most specialized science software is rather small, consequently the software is usually expensive. Many scientists even expect scientific software to be transparent (or downright free the younger they are) but how would one sustain a company in a niche market?<br />
Dan Gezelter from the OpenScience project is facing the dilemma and <a href="http://www.openscience.org/blog/?p=164">summarizes</a> the points that may have been made before but have never been...
spitshine
<a href="http://binf.twoday.net/topics/Useful+tools">Useful tools</a>
Copyright © 2006 spitshine
2006-03-13T06:39:40Z
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More on high-profile papers on protein-protein interactions
http://binf.twoday.net/stories/1680766/
The <a href="http://binf.twoday.net/stories/1664184/">post</a> on the interaction paper that I found peculiar due its stress on the "first analysis" received several comments by email and verbally. Several of them were rather disappointed with the paper in general and stressed that the body of interactions used for inferences was very small and that little novelty was described in general. However, I find nothing "wrong" with the paper and if the editors...
spitshine
<a href="http://binf.twoday.net/topics/Papershow">Papershow</a>
Copyright © 2006 spitshine
2006-03-10T18:06:07Z
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The first analysis of the human interactome?
http://binf.twoday.net/stories/1664184/
The <a href="http://www.nature.com/ng/journal/v38/n3/full/ng1747.html">analysis</a> of the current data on protein-protein interactions described in human by TBK Gandhi <i>et al</i> in the March issue of Nature Genetics delivers a fair overview - solid but yielding little surprises. The authors compare human, yeast, fly and worm networks and verify a few transfers between species experimentally. <br />
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What struck me about the manuscript is the...
spitshine
<a href="http://binf.twoday.net/topics/Papershow">Papershow</a>
Copyright © 2006 spitshine
2006-03-07T10:32:17Z
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Annotated link list
http://binf.twoday.net/stories/1657192/
A handful of noteworthy links
<h4>Other science blogs</h4>
<ul>
<li><a href="http://scienceblogs.com">Science blogs</a> - A blog network supported by <a href="http://seedmagazine.com">Seed magazine</a>, covering some 15 blogs
</li></ul>
<h4>Blogs by editors of scientific journals</h4>
<ul>
<li><a href="http://blogs.nature.com/ng/freeassociation/">Free Association</a> - Nature...
spitshine
<a href="http://binf.twoday.net/topics/Meta">Meta</a>
Copyright © 2006 spitshine
2006-03-05T21:03:15Z
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Fractals in a petridish
http://binf.twoday.net/stories/1647094/
<img src="http://static.flickr.com/42/105660664_85553be66f_o.jpg" alt="Fractal bacteria" /><br />
The <a href="http://pruned.blogspot.com/2006/02/more-gardens-in-petri.html">stunning of images</a> of simple bacteria growing in stunning patterns crossed my browser several times last week. Explore the astounding <a href="http://socialfiction.org/">Sociofiction</a> blog, one of the sources and other references from <a href="http://pruned.blogspot.com/2006/02/gardens-in-petri.html">Pruned</a>.<br...
spitshine
<a href="http://binf.twoday.net/topics/Blogs">Blogs</a>
Copyright © 2006 spitshine
2006-03-03T11:51:50Z
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On the practice of using supplementary material for data
http://binf.twoday.net/stories/1638754/
Gregory Petsko's <a href="http://genomebiology.com/2006/7/1/101">editorial</a> in Genome Biology compares the current practice of stuffing all data into tables and ill-formated text files as supplementary material and only giving an introduction and a discussion in the main paper with fighting a land war in Asia. I don't particularly like the analogy and the tone of the editorial in general but largely agree. <br />
Currently, we attach complex data to a document...
spitshine
<a href="http://binf.twoday.net/topics/Journals">Journals</a>
Copyright © 2006 spitshine
2006-03-01T18:32:27Z
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Vitamin-D mediates antimicrobial response
http://binf.twoday.net/stories/1628062/
If you are but moderately involved in research in innate immunity and Toll like receptors, the Science paper by Philip T. Liu <i>et al</i>, led by Robert Modlin entitled <a rev="review" href="http://www.sciencemag.org/cgi/rapidpdf/1123933v1.pdf">Toll-Like Receptor Triggering of a Vitamin D-Mediated Human Antimicrobial Response</a> will cross your path soon - in a journal club or on a coffee table conversation. <br />
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If your are just...
spitshine
<a href="http://binf.twoday.net/topics/Papershow">Papershow</a>
Copyright © 2006 spitshine
2006-02-27T20:08:17Z
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Fairy tales of actin tails
http://binf.twoday.net/stories/1613286/
This Valentines Day greeting depicts <i>Shigella flexneri</i> (green) and its actin tails used to escape the phagosomes of <a href="http://en.wikipedia.org/wiki/Macrophage">macrophages</a>[w]. Gullible people like me could think that the was a genuine finding - but it was photoshopped.<br />
<img width="393" height="347" title="Shigella flexneri in a macrophage" src="http://static.twoday.net/binf/images/actinheart.jpg"...
spitshine
Copyright © 2006 spitshine
2006-02-23T19:13:04Z
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