Tag Archives: workshops

World tour of workshops, recent stop: Morocco, Africa

Trainers & organizers

Last year I had the opportunity to give a workshop in Ifrane Morocco (UCSC Genome and Table browsers, Galaxy) at Al Akhawayn University. This year, Mary and I returned for a longer 3-day workshop at University Hassan II in Mohammadia. OpenHelix was a co-sponsor of the workshop (donating our time, materials and expertise). The workshop covered a plethora of topics from a world tour of resources (tutorial-free) and introductory UCSC  Genome Browser (tutorial-free) and ENCODE (tutorial-free) to genome variation analysis in dbSNP (tutorial-subscription) and analysis using Galaxy (tutorial-subscription). You can see the full schedule of the topics Mohammadia Workshop Schedule here (pdf).

As last year, we were impressed with the students (there were 117 total, about 50/50 gender ratio). English is their 3rd or 4th language in most cases, Moroccan Arabic, French or various African languages being their language of choice. Yet, they were attentive and asked very perceptive and fascinating questions. They were also very enthusiastic

The workshop students

learners. It was a delight to teach them.

We’d like to thank Mohammed Bourdi at NIH, who spent large amounts of time and financial resources to organize this (and last year’s) workshop. We hope to repeat and expand these for next year and perhaps years to come. We will be looking for sponsors.

Several questions were asked at the workshop we’d like to reiterate the answers here and seek some answers from our readers:

*One student was looking for wheat genome resources for designing primers. The wheat genome is as yet incomplete, but there are some resources to get started:
Wheat Genome Sequencing Consortium
Gramene’s wheat resources
Wheat Genetic and Genomic Resource Center @ Kansas State
Perhaps also COGE for conserved sequences
edited to add:
CerealsDB and
James’ post on the wheat draft sequence might give some insight into that huge genome.
*Another student asked about dotplot tools:
Galaxy offers a large collection of EMBOSS tools including dotplot analysis, as does EBI Emboss tool

* Another question concerned finding a ‘dynamic programming’ (optimal solution) multiple sequence alignment tool as opposed to a heuristic one. The issue with this is the complexity of the search space of dynamic programming solution, this slide set might help with the understanding, particularly slides 1-5 and 17-22. It is too computationally intensive. That said, the student might want to check out MSAProps and this list at Wikipedia.

Do our readers have any other guidance on this?

Teaching moment

* Another student asked  if we know how to find DC-area internships in biological sciences. Another student (mathematician from Mali) was looking for something in the US in bioinformatics. Any ideas of programs to bring African biology students to the US or Canada?

If our Moroccan students (or anyone else) have any additional questions, please feel free to ask them here!


ANd a side note. Last year I had all of 3 hours to tour Fes. This year I took advantage of my trip. Mary and I spent a few days in Fes and Marrakech. My family joined us in Marrakech and later my family and I toured for 8 days visiting the Atlas mountains, the Sahara and Fes. Needless to say, it was a trip of a lifetime. Morocco is a fascinating and beautiful place. I look forward to visiting again.

Gates and doors of Fes are beautiful

camel excursion to the Sahara





Workshop: World Tour of Genome Browser and Galaxy of Analysis Tools

Would like to just announce that Mary and I will be giving an all-day hands-on workshop on Tuesday, November 2nd, 2010 in Washington DC (my home town), right before the ASHG conference (where we will also be). The title of the workshop is A World Tour of Genome Browsers and a Galaxy of Analysis Tools. We’ll be covering UCSC Genome and Table Browsers, an overview of other genome browsers, BioMart, Galaxy and a tour of genome resources and how to find them. For more information on location, cost, topics you can continue reading here. There are workshops on UCSC and Galaxy at ASHG  for attendess (which we will be at, but Bob, Anton and others will be doing), but those have sold out and filled up. We are offering this workshop for those who would like to learn these topics and more, both DC residents and ASHG attendees.

To purchase a seat and register, go to our upcoming workshops page.

Continue reading

Education at NCBI

I’d like to point out the new NCBI Education page. There is a lot there that you might want to check out. NCBI will be, starting this fall, offering a series of two-day training courses they are calling Discovery Workshops. Two years ago they ended the NCBI Field Guide workshops, so this seems to be a welcome change.

There are also webinars. Our research suggests that webinars are not particularly popular, so I’m curious how these turn out. There are also ‘how-to’ guides, documentation, community, teacher resources. It’s quite a nice site with lots of things to check out.

I’d also like to point out the “recommended links” section. There are lots of links to additional educational resources like the Cold Spring Harbor’s Dolan DNA Learning Center and much more. And, incidentally :), a link to our own free tutorials which was very nice to see. You might want to check those out, we have over 10 including PDB, SGKB, UCSC Genome Browser, Galaxy, several model organism databases, and more.