Philippine-American Academy of Science and Engineering


Datasets Galore, Expensively Generated by Some but Free to the World

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1. Baltz | October 13, 2011 at 10:25 PM EDT

I listened to a very nice lecture yesterday (Oct 12, 2011) by Professor Russ Altman on Emerging Network of Data on Genes and Drugs, and was very impressed with the way he runs his research laboratory at Stanford University. His group does not perform wetlab experiments and does not generate datasets for his informatics and computational biology research. The lab members mine public online databases such as the Gene Expression Omnibus (GEO, where over 20 thousand gene expression datasets are deposited) and a US Food & Drug Administration's database on drugs and their interactions, to name a couple of examples mentioned in the lecture. Altman's lab contributes to this emerging global network of data by creating its own open online databases, including the amazing Pharmacogenomics KnowledgeBase (PharmGKB). And here's what struck me too: once their computational analyses come up with strong predictions or hypotheses, they pay wetlab scientists to do the experimental validation for them (yes, there are several credible companies now in the US that carry out focused experiments for paying customers).

I started imagining that a computational research lab similar to Altman's could really thrive in the Philippines. It will be cheap to run it. You will need a good reliable connection to the internet, to access all those free online databases - I think we have this now, which is great. You will need brains, but I'm sure there's no shortage of that. You will have to form a multidisciplinary group, with members that include savvy computer programmers, bioinformaticians and system biologists; and you must closely collaborate with local biomedical researchers and health practitioners who would inspire the group with well-focused and relevant goals. There must be a long list of health problems afflicting the local population, so being relevant should not be an issue as long as you don't get too theoretical. It might take a while to achieve critical mass, to train and educate young members, and sustain their interest. And it will indeed be advantageous to use all the network of collaborators you have outside the country. Email and video conferencing tools have made geographic location almost irrelevant today. Are there labs like Altman's that are thriving in the Philippines?

2. Baltz | October 24, 2011 at 02:48 PM EDT

Russ Altman's talk is on YouTube! Cut and paste the following


Please let me know what you think.

3. Jaclyn | November 15, 2011 at 05:20 PM EST

This atricle is a home run, pure and simple!

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