30 January 2007

New blog: Beginning Python for Bioinformatics

Beginning Python for Bioinformatics is a new blog about... (guess what). The author's aim is to convert the book Beginning Perl for Bioinformatics into pyhton.

See also: Python course in Bioinformatics


28 January 2007

Social Genealogy

From the FAQ: Geni is a unique approach to solving the problem of genealogy, which is the question of how everyone is related. Geni lets you create a family tree through our fun simple interface. When you add a relative's email address, he or she will be invited to join your tree. That relative can then add other relatives, and so on. Your tree will continue to grow as relatives invite other relatives. Each family member has a profile which can be viewed by clicking their name in the tree. This helps family members learn more about each other and stay in touch. Family members can also share information and work together to build profiles for common ancestors. Geni is a private network. Only the people in your tree can see your tree and your profile. Geni will not share your personal information with third parties.

See also, my previous post about how to draw pedigrees using DOT.


24 January 2007

Share your graph using swivel

Yesterday I found Many Eyes a service used to create and share some graphs to visualize your data, and his morning,Deepak also found Swivel which seems to be a similar product. However wile you have to copy and paste your data in ManyEyes, you can upload a csv file with Swivel.

I tried to create the same graph I did with openeyes and dbSNP yesterday, but I was not able to create a graph which could compare two columns in the same data-set, and moreover swivel doesn't stop to say "Swivel has not started swiveling this data yet. It'll be worth the wait".... and I've not time to investigate this further....


23 January 2007

Create your Visualizations with IBM's Many Eyes

Many Eyes is a new social tool from IBM used to create a custom dynamic visualization (bar chart,treemap, block histogram, bubble chart, line graph, network diagram, pie, scatterplot, stack, GIS ...) charts from your data. The graphics are plotted via a java applet. I've tested it using the snp data from the UCSC: for example, I've running the following query in the snp table:
select chrom as "chromosome",molType,class ,func as "function",avg(avHet),min(avHet),max(avHet),count(*) as "count" from snp126 where avHet>0 and valid!="unknown" group by chrom,molType,class,func

which group the snps features by chromosome, class ,etc... and I've displayed it as a treemap using Many Eyes


BioSysBio 2007

FYI: Several presentations from BioSysBio 2007 are available on google-video:



Nature Network Reloaded

Nature Network Boston(NNB) is a networking tool for scientists in the Boston area. It was created last year and I was little bit disappointed when I compared it to www.linkedin.com or www.openbc/xing.com.

Today I received this mail from NNB:

Thank you for setting up the Bioinformatics and Semantic Web groups on Nature Network Boston. I know it's been a while, but I finally have news about the website to report.

At the end of February/early March, Nature Network Boston will become part of a new website called Nature Network, which will be global in scope so we will be inviting scientists from all over the world to use the site. NNB will become a local channel within Nature Network (with local news and events).

Groups will still be there. On Nature Network, they will be labeled as either global or local (Boston-based) in scope. When we go live with Nature Network, all existing groups on NNB will, by default, be labeled a Boston group.

The other new thing going live in early March: each group will get its own discussion forum, so that group members can post messages and respond to each other. I'll send you another email in a few weeks with more details about how to be a moderator in your group forums.

Great ! I'm impatient to see this :-)

22 January 2007

Launch of BMC Systems Biology

BMC Systems Biology, the first open access journal focussed solely on the entire emerging subject of systems biology, has just published its first articles.

17 January 2007


Via pharyngula:

http://boinc.bakerlab.org/r... Explains the science behind top research on protein folding at the University of Washington's Baker Lab. 3D animations and interviews

04 January 2007

LinkedIn Answers.

The social network LinkedIn contains now a new section called LinkedIn Answers which looks like a "yahoo answers" but including the degree of separation from you to the author of a question.


03 January 2007

Bioinformation: a new forum about bioinformatics

Bioinformation, created by Mathieu Raffinot, is a new forum about bioinformatics for french-speaking people.


Nucleic Acids Research Database Issue 2007

The new annual Database Issue of Nucleic Acids Research is now available at the following address http://nar.oxfordjournals.org/content/vol35/suppl_1/index.dtl

The current issue is the largest yet and presents 68 new databases and updates of 106 existing databases.