Google Summer of Code


GSoC logo

Applications due 19:00 UTC, April 8, 2010.

The Open Bioinformatics Foundation Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for bioinformatics under the mentorship of experienced developers from around the world. The program is the participation of the Open Bioinformatics Foundation (OBF) as a mentoring organization in the Google Summer of Code™ (

Students successfully completing the 3 month program receive a $5,000 USD stipend, and may work entirely from their home or home institution. Participation is open to students from any country in the world except countries subject to US trade restrictions. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project.

The Open Bioinformatics Foundation is particularly seeking students interested in both bioinformatics (computational biology) and software development. Some initial project ideas are listed on the website. These range from Galaxy phylogenetics pipeline development in Biopython to lightweight sequence objects and lazy parsing in BioPerl, a DAS Server for large files on local filesystems, and mapping Java libraries to Perl/Ruby/Python using Biolib+SWIG+JNI. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome and encourage students proposing their own project ideas; historically some of the most successful Summer of Code projects are ones proposed by the students themselves.

TO APPLY: Apply online at the Google Summer of Code website (, where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students runs from Monday, March 28 through Friday, April 8th, 2011.

We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. See the OBF GSoC page for contact details.

2011 OBF Summer of Code:

Google Summer of Code FAQ:

Summer courses for informatics and genomics

Cornwall School House Nº 4 (1892)Here’s a few courses to consider for the summer that cover informatics, genomics, and metagenomics analysis focusing on next generation sequencing. The deadlines are fast approaching so apply soon. (There are undoubtably more, and I’m happy to post here if you have suggestions)
Continue reading Summer courses for informatics and genomics

The roundup of twittered updates for 2011-03-15

  • Colocalization of amanitin and a candidate toxin-processing prolyl oligopeptidase in Amanita basidiocarps #
  • A network approach to predict pathogenic genes for Fusarium graminearum #
  • Performance of COX1 gene to study metabolically active Pezizomycotina & Agaricomycetes fungal communities from soil RNA #
  • A. fumigatus proteome metabolic chgs & activation of pseurotin A biosynth gene cluster in response to hypoxia #
  • Allele-specific non-syn substitutions accumul in region of recomb supp on mating-type chroms of Neurospora tetrasperma #
  • Degradation of chlorinated pesticide DDT by litter-decomposing basidiomycetes #bioremediation #
  • Follow all the (sch)tweet action at the #OMGN11 (oomycete mtg) happening just before the #FGC11 (fungal genetics) #

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The passing of Walter Fitch

Walter Fitch passed away on Thursday. Below is Brandon Gaut’s message that was posted to EvolDir. He was truly an intellectual giant in evolutionary biology making key contributions to phylogenetics and molecular evolution.

Dear Colleagues –

I am sorry to report that a beloved member of our campus community,
Dr. Walter Fitch, passed away in his sleep this morning at his home
in University Hills. We will miss him dearly as a friend, as a
colleague, and as a towering intellectual presence.

Walter was born in San Diego in 1929, and earned his Ph.D. in
Comparative Biochemistry from the University of California, Berkeley
in 1958. He was a post-doctoral scholar at both Stanford and
University College (London) and held full professorships at the
University of Wisconsin and the University of Southern California. He
came to UC Irvine in 1989 as a Distinguished Professor and later
became the Chair of the Department of Ecology and Evolutionary Biology.

Walter was a founding father of the field of molecular evolution, and
established methods for constructing phylogenetic trees from amino
acid and nucleic acid sequences. He also made contributions to
virology, the origin of life, taxonomy, genetics and molecular
biology. For his work he was elected to the National Academy of
Sciences, the American Academy of Arts and Sciences and the Linnean
Society (England). He founded the Society for Molecular Biology and
Evolution and was the editor-in-chief of its journal, Molecular
Biology and Evolution for its first 10 years. He contributed mightily
not only to the intellectual process but as a mentor to young scientists.

Walter is survived by his beloved wife, his four children and several
grandchildren. Funeral arrangements are pending.


Brandon Gaut

Professor & Chair

Department of Ecology and Evolutionary Biology

The roundup of twittered updates for 2011-03-11

  • Fungal Biology Reviews makes freely available the text of Keynotes from #IMC9 (till 2012); see Vol 25, Issue 1) #
  • The poetry of mycological accomplishment and challenge, J. Taylor – #
  • The dynamic fungal cell, G Steinberg – #
  • Progress in molecular & morphological taxon discovery in Fungi & options for formal classification of envion sequences #

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Neurospora business lunch at Asilomar

[From Kevin McCluskey at the FGSC]

I am pleased to send this invitation to the Neurospora Luncheon which will be held Wednesday at the Fungal Genetics Conference. It will take place in the Chapel and box lunches will be available. This luncheon is for everyone who works with Neurospora or who wants to work with Neurospora. Please come and hear what is going on and share your opinions. It is especially important that Post-docs and students come to these meetings.

Neurospora Business Meeting


Asilomar 2011

Wednesday, March 16, 12:15 pm – 2:00+ pm

12:15 pm	Announcement of Perkins Award recipients for 2011
12:25 pm	FGSC and Neurospora meeting update- Kevin McCluskey
12:30 pm 	Fungal Genetics Reports update- Matt Sachs
12:35 pm	Neurospora e-news-  Kathy Borkovich
12:40 pm 	Update on Neurospora gene set, James Galagan - discussion
1:00 pm	Fungal Genome Database- Jason Stajich - discussion
1:15 pm  	Update on Systems Biology grant- Kathy Borkovich and Steve Osmani, James Galagan, Matt Sachs
1:30 pm	Update on QTL grant-  John Taylor and Louise Glass
1:40 pm	Update on bioenergy grant-  Louise Glass
1:50 pm	Announcement  for "Neurospora 2012" - March 8 - 11, 2012
		Scientific Program Chairs: Stephan Seiler and Matt Sachs
 	        Further discussion - topics from the floor.

The roundup of twittered updates for 2011-03-09

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Ncrassa v5 annotation released

The Missing PieceAs an update to previous post, the N. crassa annotation has been updated to version 5 on the Broad Institute website. Previously the data was not yet available for this update, but as of 8-Mar-2011 it is.  The assembly hasn’t changed but the annotation is updated and includes some fixes to improperly renamed locus names.  On the N. crassa genome site you can see files with the history of loci through this to determine if a locus name was improperly changed in the past. This should be rectified in the currently released annotation, and definitely encourage you to take it for a spin and report back to the Broad Institute if you have any questions.