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2014 September 30

Ebola genome browser

Filed under: Uncategorized — gasstationwithoutpumps @ 21:00
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For the past week, I’ve been watching the genome browser team (led by Jim Kent) scramble to get together an information resource to aid in the fight against the Ebola virus.  They went public today:

We are excited to announce the release of a Genome Browser and information portal for the Jun. 2014 assembly of the Ebola virus (UCSC version eboVir3, GenBank accession KM034562) submitted by the Broad Institute. We have worked closely with the Pardis Sabeti lab at the Broad Institute and other Ebola experts throughout the world to incorporate annotations that will be useful to those studying Ebola. Annotation tracks included in this initial release include genes from NCBI, B- and T-cell epitopes from the IEDB, structural annotations from UniProt and a wealth of SNP data from the 2014 publication by the Sabeti lab. This initial release also contains a 160-way alignment comprising 158 Ebola virus sequences from various African outbreaks and 2 Marburg virus sequences. You can find links to the Ebola virus Genome Browser and more information on the Ebola virus itself on our Ebola Portal page.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The Ebola virus (eboVir3) browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release and the conditions for use of these data.

Matthew Speir
UCSC Genome Bioinformatics Group

2011 May 13

UCSC Genome Browser webinar

Filed under: Uncategorized — gasstationwithoutpumps @ 18:13
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According to Bob Kuhn of the UCSC genome browser group:

The UCSC Bioinformatics Group announces two free webinars on the UCSC Genome Browser. The webinars will be conducted by OpenHelix, a provider  of training on many free, publicly accessible bioinformatics and  genomics resources.

The webinars (one hour and 15 minutes long) will cover the topics needed to effectively use the Genome Browser. The first webinar, to be held  Tuesday, May 24, 11:00-12:15 PM PDT, Introduction to the UCSC Genome  Browser, is designed for new users of the UCSC Genome Browser, and those who want to improve their skills at basic navigation and display.

The second webinar, UCSC Genome Browser: Custom Tracks and Table Browser  will be held Thursday, May 26, 1:00-2:15 PM PDT.

Signup required, space is limited.
For details see Open Helix:

I’ve seen some of the Open Helix training, and they do a good job.

2011 January 9

Bioinformatics training for AP bio teachers

Filed under: Uncategorized — gasstationwithoutpumps @ 10:26
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In response to my recent post on getting bioinformatics into AP bio classes, I got some e-mail:

My basic reply is that I myself am untrained in the field (as I would presume are many other teachers), so I wouldn’t have the first idea about how to implement your ideas (and therefore would not fight to support them in loud voice to the CollegeBoard).

I have no idea how to use the tool you linked to nor any of the tools that I’ve seen and tried to click through without much success (stuff at

I’m sure there are manuals / instructions out there, but with the limited time that I have, it would be more helpful to have workshops / guided instruction / youtube videos to help us learn how to use these materials.

These are all excellent points.  Let me give some existing pointers, while acknowledging the real need for a lot more.

There are currently 18 free video tutorials on using bioinformatics tools produced by OpenHelix.  Normally, their tutorials are fairly expensive (to pay the writers and instructors), but these have been paid for by the creators of the tools being taught.  (It is probably cheaper to hire OpenHelix to produce a bioinformatics tutorial than to try to create your own for a given level of quality.)  In particular, they have three free tutorials on the UCSC genome browser, and one on the RCSB Protein Data Bank (for protein structures).  I’m not a big fan of video tutorials (they always go too slow for me—I prefer books or other text-based sources), so I can’t review these.  I did once sit through a beta-release rehearsal of a live OpenHelix tutorial on the UCSC genome browser, and they seemed to be doing a good job (I have more patience for live tutorials than video ones at the same speed—I’m not sure why).

I’ve also been told that Bioinformatics for Dummies 2nd Ed. is a good introduction to bioinformatics tools for biologists, though I’ve not read it myself.  It has been used as a textbook for our Bioinformatics Tools class, which is an intro class for biologists, bioengineers, and bioinformatics students. Another book I’ve seen recommended is Bioinformatics: Sequence and Genome Analysis 2nd Ed. by David W. Mount.

There was a workshop for high-school biology teachers as part of the big bioinformatics conference ISMB 2010 in Boston last summer.  I think that something similar is planned for ISMB/ECCB 2011 in Vienna, Austria and for ISMB 2012 (which I think will be in Long Beach, CA).  There are many summer bioinformatics workshops taught at various colleges (none at UCSC, though), but I don’t know of a good list of them.  There is a short list of  online courses, and a longer list of degree and certificate programs, both maintained by ISCB (though relying mainly on providers to submit and update the entries).

There is a collection of pointers to resources for high-school teachers started at This site clearly needs to be expanded with more lesson plans, in-class exercises, homework exercises, and other teaching tools that can be quickly adopted by AP bio teachers. I’ve had a couple of teachers tentatively offer to share stuff with me, but clearly we need a site that can grow quickly and be easily maintained.

I have had a few teachers send me e-mail offering to share material with me that they have created, modified, or used.  This is nice, but I don’t teach AP bio, so can’t use the material directly.  It was not clear in some of these e-mails whether the teachers were willing to put their material in a public place where other teachers could access it.

I’ve never designed a site for multiple teachers to share their work, and I don’t know what would work best. What formats are existing (if any) documents in?  what formats would a teacher want from others?  Would a wiki (probably with registration required to change things) be best? A moderated forum? a multi-author blog with associated materials?  Would it be best to do a blog/website through a neutral party (like or set it up sponsored by a professional organization like the ISCB? I’m still trying to think these things through and get something set up.  What do readers here think would help AP bio teachers most?

Some sharing of pointers to information currently exists on the ap-bio mailing list maintained by the College Board, but little of that is related to bioinformatics (AP bio covers a lot of ground, after all), and the mailing-list format means that pointers are hard to find.


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