Added a new Favicon for those who bookmark the site... prettier that way, especially on the Firefox Bookmark Toolbar! Hope you like it :)

I'm also looking to implement a forum, but I don't know if enough traffic pass by yet (I don't want to host one of those 2-posts-by-the-webmaster forum, if you know what I mean). It would be bioIT oriented with a little biotech here and there... something to build a community around. Show your interest in the comment section!

LifeScience Insights released their "Top Ten List" (registration required) of predictions about Life Science in 2005. They focus on the IT division of Life Science (computational biology, bioinformatics, bioIT). Overall the predictions are positive, especially for bioIT (see #4), but I can't say I agree with a part of their top 10 (points #2 and 7, in particular). The whole top 10 is available in the full post! Note that they also have an overview of bioIT for 2004.

Interesting article on Biomed Central. siRNA are getting big in the research world; they allow to easily (and most of the time, specifically) knockdown expression of a gene by 50-95%. They are extremely usefull to study protein functions, but they also show lots of promise in therapeutic applications.

An article on Reuters nicely summarize the state of the Canadian Biotech sector. Promise of growth (or should we say recovery) of the Toronto Stock Exchange health sector rely on 30 or so Biotechs successfully delivering products they are developing.

Finally home... the meeting was kinda nice, except for some minor points. First, no posters, only oral presentations... so our chance of interaction with members of other teams was minimal. Second, my presentation crashed! Note to self : don't encode fancy movies in DivX when not presenting with my computer... their laptop didn't have the proper codecs and displayed blank placeholders :( Next time be sure I'll be bringing my own laptop along... It was informative to see the projects of other AIDS Quebec-based teams, at least, and we sure had lots of fun (rented PT cruiser + crazy students, guess the rest :)).

Just a little post to inform you that I'll be away for the next 2 days. I'll be attending (and doing a little presentation) a provincial AIDS research-oriented meeting. I'll be back posting news on saturday!

The MathWorks just released version 2.0 of their MATLAB Bioinformatics ToolBox. Its a set of bioinformatics-related functions allowing to do various tasks, ranging from microarray data normalization, visualization and analysis, protein, DNA and RNA sequence analysis, phylogeny, data retrieval from the web databases, etc. Its similar to Accelrys GCG Wisconsin package, but a few key differences should be noted.

Agilent and ExonHit Therapeutics announced a research partnership aiming to allow detection of gene splicing variants. Alternative splicing allow for different proteins to be produced from an unique gene. Its an additional layer of biological complexity that we're only beginning to understand.

Along the lines of the Human Genome Project, and related to our previous story about a potentially imminent pandemic of Influenza, The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), announced yesterday their Influenza Genome Project.

NASA isn't just about rockets and Mars-crawling robots... The NASA Ames Research Facility just published a very interesting genomics study. They designed High-density Microarrays, based on the recently "finished" Human Genome Project, using their Maskless Array Synthesizer (MAS) system (manufacture of Affymetrix arrays use mask-based lithography). 134 arrays and 52 millions unique probes (spaced on average 46 nucleotides apart, spanning 1.5 Gb of non-repetitive sense and antisense genomic DNA) later, they had a "map" of the entire genome. These tiling arrays were then used to determine experimentally and with great precision the regions expressed as RNA (in liver tissue), corresponding to genes (and all their splicing variants) and microRNAs (or something else yet to be identified).

According to the World Health Organization, an Influenza Pandemic is incoming. This is unrelated to the fact that there is a shortage of influenza vaccine in the US (The vaccine in short supply is targeted at a different strain than the feared pandemic-causing one). Vaccine-producing companies throughout the world scramble to design a solution against the strain H5N1 ("H" stands for Hemagluttinin and "N" for Neuraminidase, two viral proteins), who could migrate from birds to humans with devastating effect. Should we be scared?

Long posts cluttered the main page, so I implemented a summary/link combo for them. You can always click on the post title or the "Read more!" link to get the whole story. Plenty of advantages... the main page is less cluttered, so you can see past posts more easily. Ads are more targeted everywhere, so they are more relevant to your interests. Speaking of ads, I finally fixed the problem with Adsense! thescientistblog.blogspot.com got Public Service Ads (non-paying, untargeted, which I replaced with Amazon Bioinformatics Books) while www.thescientistblog.blogspot.com got targeted ads about bioinformatics, AIDS, HIV and biotech in general. So update your bookmarks according to your preference!

This week Genomatix released version 3.2 of their excellent promoter-analysis software, GenomatixSuite. This follow their last month release of the new and improved GEMS Launcher 4.0. According to the press release, new features / improvements include...

Trinity Biotech, an Ireland-based company, issued today a press release announcing that they just got FDA approval for being used in doctors' offices and clinics. Previously, it could be used in the hospital environment only. Why is this important?

I received a mail informing me that TOUCAN, a regulatory sequence analysis package, just released a new version. More importantly, they've gone Open Source, which is good. I tried version 1.0 last year and had mixed feelings, notably about the Java interface. Version 2.0 brings lots of improvements on this side (the interface is still ugly, but its more functional), among other things. The feature set is impressive for anyone doing promoter regulation studies (automatic promoter retrieval, TRANSFAC database querying, overrepresentation analysis, etc). I pasted the announcement of the release, which include a changelog.

My friend Daniel over at Bioplanet
asked me to publish a (very good, in my opinion) Ph.D. opportunity.
Genomics and Bibliomics are currently very hot subfields of
Bioinformatics. Here's the ad...

PhD
Studentship at Cardiff University, UK
The PhD title is "Application of improved automated text mining to
cancer transcriptome datasets" and centres on the development of
improved mechanisms to mine gene-associated metadata (PubMed, OMIM,
etc) associated with groups of genes identified through mass-parallel
'omic techniques. It will use real datasets that are being produced on
the Affymetrix gene expression platform through our CRUK Programme
Grant, but the techniques would be generally applicable to other
techniques (e.g. proteomics, Taqman arrays, etc).
The student would join a small but active bioinformatics team and the
other members of the CRUK Programme in our new Henry Wellcome Building
at the School of Medicine. It would particularly suit a student with
existing mathematical, statistical or computer science skills who
wished to broaden their experience into the biomedical field. Further
details of the studentship can be found at:
http://science.cancerresearchuk.org/gapp/grantapplications/tcdb/tcd_phd

Supervisor: Professor David Kipling
Contact: KiplingD@cardiff.ac.uk

Syrrx, a drug design company, just released the 3D structure for their main target, human 11(beta)-hydroxysteroid dehydrogenase type-1 (HSD-1). Inhibitors of this enzyme have potential in the treatment of type II diabetes. Why is this interesting? Consider the drug design pipeline :

Just came across Zlabs Gene Regulation Tools, a site regrouping links useful in gene regulation analysis. Promoter databases / extractor, overrepresented motifs finders, promoter prediction, microarray analysis, phylogenic footprinting, it have it all. Great portal, be sure to check it if you're in this kind of stuff! I'm adding it to the "Tools" section right now. As a side note, I entered the BioBanner program to replace Google Adsense ads when they go non-targeted (The "Save Gorillas" stuff, great cause, but no ad revenue from those, sadly). Its an banner-exchange initiative put up by the folks at bioinformatics.org for biotech related website. Let's hope that it'll increase incoming traffic up here... and let's hope the Google bot recrawl the page soon.

There's been a lot of talk about the (over)hype of bioinformatics as "The Way of The Future" and the apparent lack of concentrated effort / funding to justify the media buzz... creating lots of uncertainity / discomfort in the field. Well, good news are on the way...

Redesigned the site banner... the virus was too fuzzy for my taste at a resolution that low. Removed the texture on the text too, as it was too distracting / not enough crisp.

Sorry for that last triple post, it seems Blogger got unresponsive last night (it just came back up) and did all kind of crazy things. Everything is fixed now, so we can get back (soon, got infections to do!) publishing news :)

VIBE (Visual Integrated Bioinformatics Environment) from Incogen just got released for Mac OS X. Previously, it was available for Unix and Windows platform only. Apple being popular within the scientific world (for some obscure reason I can't quite explain) probably justified the move. In case you wonder : "The INCOGEN Visual Integrated Bioinformatics Environment (VIBE) is a state-of-the-art, drag-and-drop analysis workflow management environment." If you wanna see VIBE in action, a tutorial flash video is available. Basically, its used to build a data analysis pipelines with little to no effort. A powerful drag/drop interface allow you to build graphically pipelines, with conditions / parallel analyses. Its a lot better than scripting command line functions. Of course, only labs doing high throughput sequence analysis (lots of BLAST, FASTA, Gene prediction, etc) can justify buying this software (it isn't exactly cheap), but its interesting to see that Mac still has developers attention in the bioinformatics world.

As you may know, I have a special interest in Bibliomics (science of scientific litterature). When you're analysing microarray results, you're confronted with a big list of modulated genes, and you want to extract the biological signification of it. The main source of information is Pubmed by far, but genes (and proteins) often have 5-10 synonyms... multiply this by 200 modulated genes, calculate the number of pairs of genes to look at (to see if known interactions exist), and you got a big problem. Fortunately, bioinformatics programs to ease the pain just start to show up. You may already know Bibliosphere, by Genomatix. Quite excellent, but has its limitations (the number of analysis / month is limited). Enters Chilibot (OK, lousy name). Noticed the article describing its conception in BMC Bioinformatics last week, and had to try it. And let me say, its wonderful. Not perfect mind you... but close. You give it a list of genes AND/OR biological concepts (apoptosis, T-cell, HIV-1)... it finds automatically ALL synonyms and perform pairwise searches on Pubmed, then output the result in a very nice graph. Free. On the Web. Try it. Now!

Elections Day in the USA... MY GOD its a complicated process! Up here in Canada we vote for our deputy... and thats it. They vote for their president, senator, governor, house representative, a few state-dependant bills... by punch card, electronic voting booth... Honestly, I'm looking at the various maps on CNN.com, and I wouldn't have a clue if I had to explain the whole system. Canada 1, USA 0!

Important stuff aside, it seems that the province of Quebec wants to develop its (economic) relations with India, especially in the bioinformatics area.
The article state an obvious barrier : Indians can speak English (not
fluently, but oh well; personal judgment, from most indians posters in
bioinformatics boards), but can they speak French fluently? Immigration
laws in Quebec favorise (by far) french speakers with a good skill set;
for this reason, most Indians coming in Canada choose Toronto or
Vancouver. Even if they wanted to come here, quite frankly, I don't
know what to think about it. Wouldn't be more productive to exploit the
pool of non-working IT workers (coming from the dotcom era) up here
than to go fetch some across the globe? Globalization they say... I'm
not sure its a good thing in the long term.

The New York Jewish Times reports that a NIH-funded study, published in PNAS last month, unveiled some smallpox secrets using microarrays. As you may know, smallpox is a potentially deadly virus who have been eradicated thanks to an extensive vaccination campaign. The only problem is that my generation (young adults) wasn't vaccinated and authorities fear that smallpox could be intentionally released by terrorists organization as a biological weapon (it would cause more fear than harm, but anyway). The only time it has successfully been used as a weapon of War was in 1754-67, by British forces who gave infected blankets to native Americans; some tribes lost 50% of their population.