Category Archives: education

Vote for some Fungi in Open Tree of Life project

Consider voting for for some Fungi in the Open Tree of Life project. Pathogens, model systems, and any charismatic (or non-charismatic if like) organisms can be proposed to be included in a tree that will serve as teaching and communicating the tree of life.

[From Laura Katz]
Dear Colleagues,

We need your help creating a list of exemplar species from across the tree of life!

As our team works to build an open tree of life for the systematics community, we are also working on an educational version of the tree for the public. Our goal is to depict about 200 better-known (i.e. phylogenetically or otherwise important in some way (pathogen,
food source, etc.)) species from all three domains of life. The intended audience of this effort includes educators, students, and the public in general.

Please follow the link below to vote for your 5 best exemplars…

And please join the conversation through our website, email (, or twitter (@opentreeoflife).

Thank you!

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:

In bookstores now

I am excited to dig into the newly published Cellular and Molecular Biology of Filamentous Fungi edited by my next door neighbor Katherine Borkovich and Daniel Ebbole from Texas A&M which was recently published by ASM Press.  The book is a comprehensive look at biology of filamentous fungi including ascomycetes and basidiomycetes and covers cellular biology and structure, metabolism, growth, organelles, photobiology, sexual and asexual development, and mutualistic and pathogenic interactions with plants & animals.  I’ve yet to get my own yet but I’ve leafed through a copy and this looks to be an excellent reference for those wanting a review of current knowledge on many aspects of fungal biology and I anticipate important reading for new students and postdocs in the field.

Really involving undergrads in research

A paper in Genetics today has many, many (!) authors — and they aren’t from a big multi-nation project or large genome sequencing center, but a collection of undergraduates at UCLA. Maybe they didn’t all write the paper which can be confusing to some folks, but it looks like a group effort lead to some important results.

Using a large consortium of undergraduate students at UCLA in an organized program, we have undertaken a functional genomic screen in the Drosophila eye. In addition to the educational value of discovery-based learning, this report presents the first comprehensive genome-wide analysis of essential genes involved in eye development. The data reveal the surprising result that the X-chromosome has almost twice the frequency of essential genes involved in eye development as that found on the autosomes.

I am sure there are probably several other examples of this type of hands-on research education ongoing at different universities large and small. It is great that it can lead to a publication for these students and hopefully get them excited about problems in biology and genetics. Now let’s get those Neurospora screens going for undergraduate class projects!