February 20th, 2009
Here’s the deal:
Meet local folks interested in bioinformatics, computational biology and Web 2.0. Talk to people who love combining Life Science with Computer Science to see what happens. The name comes from the Life Scientist group on FriendFeed.
Let’s chat about the future of science on the internet and the current trends in the biotech industry.
Personally, I’m interested in the computational biology side of things. How can we push molecular simulation techniques and high performance computing to the point where rational drug design becomes routine?
I also link to think about the future of science and scientific publishing. How can we (programmers and techies) develop the tools that the next generation of scientists will use on a daily basis? How will we make publishing more efficient and peer-review more transparent? How will we create incentive for people to collaborate?
Palo Alto Life/Computer Scientist Meetup
Date + Time: Tuesday, March 3rd 2009
Location: The Prolific Oven (Palo Alto)
Cost: Free!
If you have suggestions comment down below or on FF or send me an email.
david |
Bioinformatics, Computers, Science, Silicon Valley |
August 15th, 2007
I spent a couple of months this year working on a web-based “script platform” for a lab I was working in. The idea came from the issue that most scientists are afraid of the command line, so why not make an easy way to turn a perl script (or any script for that matter) into a web app?
Script-o-matic (ok the name sucks, I know) was designed for that purpose. The app is written in PHP using the Symfony Framework (like Rails but for PHP). There are three main parts of the app: My Data, My Scripts and My Actions.
My Data allows uploading of files to the server (stored in the DB). It supports revisions of files right now.
My Scripts is where the magic happens. Admins (read: bioinformaticians) take a script and turn it into a PHP class that inherits from a certain PHP class so that every script is run the same way. Basically, the PHP class will have a unique name, and an execute() method called by the web app. The execute() method can run any piece of code, if it’s PHP written right in that function or another script or a whole pipeline called by PHP’s system(). Anyways, the class also gives the web app access to the data returned from the script (or whatever set by the programmer). The “script” class is organized in such a way that it tells the web app what kind of input/output it requires, and tells the app to use pre-written “parameter” classes for each type of input/output (for example, textarea or checkbox). When a script is loaded by a user, it autogenerates the web form based on the script! pretty cool stuff.
The last section, My Actions, keeps a log of any script that has been run and with what input/output data (lab book style). The app also is user-oriented, and users must login to use it. My lab was using LDAP authentication for the users, but anything can be used.
See the image below for a flow-chart of the app. I would be that something like this exists already (sort of like Taverna or something), but I couldn’t find it. Let me know if you know of something similar or if my explanation is unclear.
The first version of the app was written in about 2-3 months and is definitely not perfect but it did work. I am currently re-writing it and will give updates on my blog about it. I am pretty sure lots of labs could use it.
david |
Bioinformatics, Computers, Science |
August 14th, 2007
Another eye-opener with some food for thought. I was just watching Esther Dyson on Charlie Rose, an interview on her takes about emerging technologies. First she was talking about how she is “over” social networking sites, not that they are over with, but that she doesn’t want to invest in them anymore. She goes on to talk about how Facebook is the “next Google”, and how their platform has enabled an instant user-base for new apps (which it definitely has). She mentions later how the next big move is into health care, both on the “street level” (doctors, medical data) and on the research level (genetics, raw data analysis). I am now convinced (call me crazy) that Google is probably going to release Google Health (now buzzing around the net) and later write apps for bioinformatics analysis, or at least very nice data presentation. I think it is about time bioinformaticians (myself included) get their act together and make some web apps or Cocoa apps that are easy/fun/rewarding to use, nice to look at and very functional (ie: well designed software).
Mrs. Dyson even spoke about a new project involving about 10 investors dealing with sequencing individual genomes (including her own) and a few other geneticists. Who knows what they are working on?
david |
Bioinformatics, Computers, Science |
August 14th, 2007
Today I went to the Montreal Tech Entrepreneurs Meetup with my friend David Gross. I was amazed about both the number of people attending and the diversity of the qualifications/skills/experience that people had. There must have been at least 2 or 3 VCs there (if not more) and at least 10 hard core developers/IT people (of entrepreneurial type, of course). It is a perfect place to bounce ideas off people who understand both business and IT concepts. Unfortunately I had to leave early because of a very important business meeting (AKA dentist appointment) but I definitely should have gone to a few more.
I’ll be leaving back to Calgary in a few weeks and I would love to try and get one started there, just have to think about a good enough restaurant (maybe something near Kensington or 17th) and talk to a few people. I will be attending the 3rd Calgary DemoCamp, where I’m sure I’ll meet some interesting people.
I was also thinking about starting a science-based BarCamp-like open conference, maybe for bioinformatics or neuroscience? HippoCamp anyone (not as in sea-horse) ?
david |
Computers, Montreal, Science |
August 12th, 2007
All this talk of open science and scientific culture has got me going a bit. My relatively short experience (about a year) of being a so-called bioinformatician has revealed a lot to me about how labs seem to work. I’m not going to go into how I think research is broken because I’m sure everybody already knows…
What I wanted to write about were my thoughts on the “new culture of science” that is starting to pop up everywhere. The underlying thought is that science needs to have a major change across the entire community. I really think that this is impossible (almost as hard as trying to convert the USA to communism), but I think there is still time to try new things.
A few reasons why I think it is too hard to shift to open and collaborative science:
- most labs just have to get grants, and nobody gets money (as of right now) for the time they spend helping other labs.
- most biologists and other lab techs are not as computer literate as us bioinformaticians.
- it is pretty damn hard right now to share raw data between labs, unless it is on an online repository already.
- even if you could share data, not every lab has a dedicated bioinformatics specialist to work on foreign data.
- few labs (correct me if I’m wrong) have adequate data storage and management facilities.
- once again, few people have an incentive to collaborate. You don’t get any points for it, so why do it?
I’ve been thinking about all this, and I feel that it might be worth trying out some sort of online social network beast for scientists (start with bioinformaticians of course…). Scientists will have profiles (not personal, only work) where they can exhibit their skills and show their publications. The network aspect will show collaborator networks, who has worked with who. It will also allow for criticisms of papers and people (anonymous allowed too?). The site will also have a lot of statistics, showing a scientists rank in terms of their collaboration history and papers, maybe some sort of points system (as incentive).
I think this kind of thing would never work for the majority of biologists (ahh another website?!!), although I could be very wrong.
That’s why I think it could be very useful to bioinformaticians, especially those who work in a freelance/contract sort of way to get new clients.
Anyways, something to think about. I would love to get some comments/criticisms from you.
david |
Bioinformatics, Computers, Science |
