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 .

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 ). 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 ? ). 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 . And maybe I can teach a bit too.

• A bit of a dust-up at ScienceBlogs as they added a corporate blog (Pepsi writing about nutrition science) and several of the bloggers left or threatened to leave. The Pepsi blog is no more. I hope that’s resolved, ScienceBlogs is an excellent collection of science writing. [Trey]
• Pathway Tools Workshop 2010 held by the folks from BioCyc announced for October 21-25: http://bioinformatics.ai.sri.com/ptools10/ [Mary]
• Animal portraiture against a white background. It’s been done before, this time with birds. It always reminds me how amazingly beautiful life can be. [Trey]
• VectorBase announces that they have moved to the new style Ensembl browser with their current release–Yeah!  If you are interested in “Invertebrate Vectors of Human Pathogens”, this database may have species you want to know about. [Mary]
• A good discussion about the recent ‘longevity gene’ study and it’s possible flaws by Razib Khan of Gene Expression [Trey]
• Bandwidth-heavy, but really neat movies of tumor angiogenesis. You can open the Navigator menu to see the various movies listed, or you can migrate around the tumor yourself.  Hat tip to Jill!  [Mary]
• On the GBrowse mailing list people were looking for examples of GBrowse 2.0 in action. WormBase indicated they are up to that version, and there was another research group with a species I never heard of before that also has it running: Gardnerella vaginalis.  They have compared 2 strains: one from a healthy woman, one suffering from infection. They show divergence, interestingly.  You can check out their recent publication on it from their publication tab.  A nice demonstration of how to use GBrowse for your species of interest. [Mary]

Interlocutor: “So what do you do?
Me: “I’m a librarian.”
Interlocutor: *lengthy pause* So… what are you doing here exactly?

Er, what? A conference about science communication? How on earth can that not be imagined to intrigue a librarian?

This, ladies and gentlemen. THIS. Right here. This disconnect is the number-one threat to science librarianship today—perhaps to all academic librarianship. How can science libraries persist when scientists haven’t the least notion that libraries or librarians are relevant to their work?

I noticed a similar discussion going at STELLA (manifested in topics on embedding, the library of the future and science 2.0). My basic take on this is that researchers are are going to need physical libraries less and less (do they really need them now?) and librarians more and more (but they don’t seem to realize that). I commented as such on the post above.

Deepak Singh has asked a similar question today, and started a discussion.

But impact factor measuring has it’s issues (Article-Level Metrics and the Evolution of Scientific Impact, Neylon and Wu. PLoS Biol 7: e1000242), and there is always a search to measure the impact of journals and individual articles better, or at least differently. Well, one of my favorite science sites and one of my favorite journal publishers ResearchBlogging.org and PLoS, have worked together to measure the impact of journal articles. PLoS has a lot of metrics to see what the ‘impact’ of an article might be, and now they’ve added a metric to see how many times it’s been written about on blogs using blog aggregators like Postgenomic, Blog Lines and Nature Blogs, and now ResearchBlogging.

I like the partnership with ResearchBlogging specifically because whereas the other blog aggregators are not necessarily picking up articles that discuss the science of the article (Postgenomic) or aggregate only a subset of science blogs out there (Nature Blogs), ResearchBlogging is specifically blogs posts discussing the research of  peer-reviewed articles.

Of course I don’t find this particularly useful to compare one article against another (the best articles aren’t always written about, and those that are might not be in the blog aggregators), but I do think this will be great way to carry on the conversation and dig deeper into the research topic.

You can view that metric at PLoS of any article, for example the one I link to above, click on the “metric” tab, scroll down a bit until you see the heading “Blog Coverage.” For that article, you’ll see two ResearchBlogging posts (as of this writing), a metric for this paper about metrics .

I use the iPhone for a lot of things, directions, finding out what stores are in the area, keeping my grocery list, listening to music, watching shows, browsing the web, keeping my calendar and contacts and a bunch more. Oh, and to make and receive phone calls .

I’ve read past posts on other blogs about scientific apps for the iphone, I decided it was time to check out what apps there are now.

I’ve found a few I like, some that might work (I do computational genomics now, so I haven’t tried the ones for the bench), and one that has nothing to do with biology (directly anyway), but I am in love with. Follow me below the fold.

First, there are several apps that access pubmed for searching. Ok, so I guess you could just use the browser, but then it’d be ugly and not work quite as fast .

So, I checked out three (links open up iTunes page for the app):
PubMed on Tap
PubMedSearch
NextBio

The first two on the list do basically the same thing (I used the paid version of both, 2.99 and 1.99 respectively). They allow you to search PubMed, obtain full text articles as PDFs (including subscribed journals using your universities proxy), email articles and keep a library of them on your iPhone. The functions worked on both for the few searches I did, I couldn’t test out the university library proxy access to full text, but of course it works with opensource text. And according to the reviews, as of this blog post, PubMedSearch seemed to be sporadically working). As to the interface and ease of use, I’d give PubMed on Tap a 4/5 stars, PubmedSearch perhaps 2.5. It’s worth the extra dollar for PubMed on Tap.

NextBio is somewhat different, it uses the NextBio services database of experiments, clinical trials, news and literature to search. The app is free. If I was a medical researcher or clinician, I can see this app being useful (a search for Huntington’s disease found interesting articles, experiments and trials). As a PubMed search, it isn’t exactly up to the functionality of the two above (couldn’t retrieve full text or email results), so if I was using it just for that, again, I’d go with PubMed on Tap. Though, again, for _my_ purposes. I can see NextBio possibly being very useful for the above mentioned researcher.

There are several apps I found that might be useful for experimental biologists, though I couldn’t really test them out, since I don’t do bench work any longer, but I could see the utility (no review, I did not buy them):

Primer Jot (1.99)
iCut DNA (4.99)
Solutions (0.99)
Molecules (free)
LabTimer (free/2.99, same functions, kind of a shareware model)
Genome (0.99)

Primer Jot is a place to categorize and store information about the PCR primers you are using in your research with melting temperatures, sequence, physical location, etc.
iCut DNA  allows you to search REBASE for restriction enzyme data.
Solutions. I could have so used this one during my Ph.D. I was always making mistakes in creating solutions. It calculates the weight, volume and molarity of chemical solutions, uses the PubChem and Chebi database and does a few things I could have found useful.
Molecules is a 3D protein structure viewing app that allows you to turn the structure, zoom in and more. Cool app. Can’t beat the price.
Labtimer: here’s another I could have used. Ok, so I had a lab timer, but it would have been nice to have anyway. Then I started to think it would be good for a kitchen timer (or cooking different steaks at different doneness so they all come out at the same time ), then I remembered I used a kitchen timer in the lab, then I checked kitchen timer apps on iTunes: 5 in 1 Kitchen Timer
Genome: More of an educational tool than something I could see using often in research, but it has a codon table, translates and transcribes short sequences, etc.

This last made me think though, I didn’t find much in the way of iPhone apps specifically interfacing many of the databases out there. It seems the iPhone (and mobile computing) is ripe for such apps. Of course Illumina had a ‘concept’ app they suggest for viewing your personal genome .

I’ll point out two other to leave you with, not particularly research-oriented, but…

Pocket Universe. I’m in love. We are spending over a month on the Big Island of Hawaii, a major location for stargazing and astronomical research (and an _excellent_ new astronomy center). Yes, I know, you feel sorry for me. We went up to the mountain to stargaze. I had a starmap, but it wasn’t optimum. This app though. Wow. With the 3Gs (GPS, compass), the app would show you the night sky exactly where your location and time were, then, as you moved the phone, the view on the phone would change to the location you were looking at in the sky showing you the constellations, star names and information, planets, etc. There’s much more to the app, but that had me gazing at the stars… didn’t have much time to look at much else .

Check out PhDComic if you need some laughs to get you through your graduate studies, or if you just want to reminisce about your studies from a safe distance of time . (unfortunately, not working for me at the moment on my iPhone, but I can read them on the web).

Any other apps you’d suggest? You have? You have an idea for?

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You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

{I’m closing comments here since a fresh thread is up–Mary}