Tag Archives: Morocco

My “View from Your Window” photo in Casablanca

Just a fluff post, tangentially related to genomics because we are in Casablanca recently and it’s about a photo I took there :D.

I read Andrew Sullivan often. Every Saturday he has a “View from your window contest” where he posts a photo a reader has submitted that was taken from a window. Readers have till the next Tuesday to send him their guess.  He posts these photos daily and has a book of them, which he gives to the winner of the contest.

Well, on our recent trip to Morocco , I took a photo out of our hotel room window. I took one look at it and thought “VFYW contest!” So, I submitted it. I was pleasantly surprised to find that he used my photo this Saturday. I eagerly awaited the readers answers today, and wasn’t disappointed. There were several guesses, several which got “Casablanca” and the right hotel. The winner actually got the right floor (6th).

Two ‘regrets’… one, in my email to him sent from my phone, it autocorrected “meet” with “moment” so the sentence “my family moments me tomorrow to take a trip to Marrakech, Fes and the Sahara.” should read “my family MEETS me”. Oh well. ANd if I took that photo with an eye to the contest, I would have shifted a bit to the left so “TEGIC” didn’t show up :D. It was a give away.

Though, I can NEVER get these. Sometimes I get the right continent, but his readers are pretty good at plant species, car models, architectural history, google earth and a bunch more. I’m amazed at how well they guess every week.

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





Moroccan Science

Al Akhawayn University, Ifrane Morocco

Last week I attended and taught a workshop for the Moroccan American Society for Life Sciences (Biomatec-US) at their 2nd International Workshop and 9th Annual Meeting, in Ifrane Morocco.

I was thoroughly impressed. Impressed with Morocco, Moroccan Scientists and Moroccan students. I had the opportunity to interact with all three. First this students. I taught three workshops, including a tour of genomic resources and two how-to’s for the UCSC Genome Browser and Table Browser. All were enthusiastically received. But more than that I was impressed by the enthusiasm these students showed for genomics and bioinformatic research. After each talk and later in the day, I was barraged with questions and requests (which I love). Their enthusiasm for science matches or surpasses any other group of science students I’ve met in my 20+ year career in biology. In addition to that, I met several students who I was able to discuss their research with a bit.

Also, I was able to discuss research in Morocco with several Moroccan scientists informally and attend a roundtable discussion about advancing Moroccan science, specifically biological and bioinformatics research. Moroccan scientists, both within and outside of Morocco, are doing worldclass research, including my host of course. The research done within Morocco and by the Moroccan ‘diaspora’ of scientists (there were Moroccan scientists from the US, Europe and the Middle East there), seems to be a ripe network that, together with the enthusiasm of the students, is a great resource for that nation.

If the level of research and enthusiasm of the researchers and students are any indication, Moroccan science will be making great strides in the years to come. Of course, this isn’t anything new I’m sure, just new to me :D.

I learned (relearned) two things on this trip. The world is very small, and very big. I met several people who with whom I had crossed paths with before or who we had mutual friends. There was the Moroccan scientist who I briefly met in Germany while doing a postdoc there and the Moroccan student who knew someone I knew from Qatar. I was asked to talk briefly and the roundtable discussion and I mentioned a virtual African conference I had given a workshop at, and that I thought there was a Moroccan hub at that conference. Sure enough, one of the scientists at the discussion had attended my workshop (and had good words for it :D). Ok, you might say, that’s the ‘world’ of science. Well, it got down to even the woman I met in the hotel who was a Fulbright scholar doing research on Berber and Arabic music… and the man who gave me a ride from the conference the last evening, who just happened to be her Moroccan supervisor.

And it’s a huge world with a lot to discover and awe my sometimes jaded self (rarely, but I can be there). I never had heard of Argan oil before,

Street & shops in the medina of Fes, Morocco

traditionally produced from seeds collected from the feces of goats (today it’s more likely collected and processed by more modern methods :), or even considered touring the magical medina of Fes (to which I MUST return). I had no inkling of the existence of Al Akhawayn University in Ifrane, a small liberal arts school in the cool (it snows) mountains of Morocco in Ifrane (why do I want to keep writing that as iFrane :D? ). Beautiful campus.

The other thing that came to mind while attending this conference and speaking with Moroccan scientists is the potential (and unnoticed reality) of the research possibilities outside of the US-European-Japanese triangle. Of course India and China are producing great research more and more over the years, but there are another 100 or so countries out there with another few billion people with huge potentials. Of course these smaller countries have always produced great scientists, but I was beginning to think that genomics and bioinformatics is beginning to assist smaller countries ‘leapfrog’ biological research much as cell phone technology allowed some developing countries to ‘leapfrog’ from traditional telephone lines (expensive, hard to do) to wireless (less expensive). Biological research has traditionally be resource intensive: labs, larger universities, equipment. Bioinformatics and genomics research, though still requiring infrastructure, has a lower barrier of entry I believe. I made a comment in my talk, “There is no lack of data,” and it’s true. The amount of data available for analysis is staggering. The number of publicly available tools and databases is overwhelming. One doesn’t have to do “big science” in genomics (though there sure is that) to do world-class research. Thar’s research gold in them thar data hills (sorry for the reference to the California gold rush, I _do_ live in what was the center of it all). Gold that can be mined by any individual, lab or nation with a bit of education and enthusiasm.

I hope to return next year to Morocco and next years conference. I have a lot more to learn :D. And maybe I can teach a bit too.