• Log in with Facebook Log in with Twitter Log In with Google      Sign In    
  • Create Account
  LongeCity
              Advocacy & Research for Unlimited Lifespans


Adverts help to support the work of this non-profit organisation. To go ad-free join as a Member.


Photo
- - - - -

Article: Open Source Bioinformatics


  • Please log in to reply
2 replies to this topic

#1 maestro949

  • Guest
  • 2,350 posts
  • 4
  • Location:Rhode Island, USA

Posted 18 February 2006 - 09:22 PM


The awesome quantities of biological data that are piling up in just a few short years is every software engineer's/data analyst's dream! Woohoo? Not entirely. More like hmmm, where do I start?

Dozens of websites. The same tools that do the same thing written in many different programming languages and models that when lined up next to each other have a significant impedence mismatch. Databases with the same data modelled differently in each. Few standards, quantitative and qualitative differences in techniques and resources gathered abound. Oh no. The cats need hearding.

This articles sums it up nicely...

Time to Organize the Bioinformatics Resourceome

#2 maestro949

  • Topic Starter
  • Guest
  • 2,350 posts
  • 4
  • Location:Rhode Island, USA

Posted 10 June 2006 - 12:41 PM

In an effort to fight back against the stifling effect of scientific knowledge being kept under wraps, researchers are creating an open-source community that allows them to advance science by sharing data.

Article: Open Source Bioinformatics

sponsored ad

  • Advert

#3 Mind

  • Life Member, Director, Moderator, Treasurer
  • 19,076 posts
  • 2,000
  • Location:Wausau, WI

Posted 31 August 2009 - 06:23 PM

Sadly the original link maestro posted seems to have gone dead. Here is another open source bioinformatics attempt. Sage Bionetworks.

When he and other scientists in his field began their work, biologists had long thought that common diseases like cancer and heart disease could be characterized by identifying a single cause — perhaps an errant gene — and treated with a drug aimed at that gene, or, more likely, the protein the gene produced.

Some of the drugs developed that way were great successes, like Herceptin for breast cancer and antiretroviral drugs to treat AIDS. But these are the exceptions. According to a 2004 study in Nature Reviews, 89 percent of drugs that enter human clinical trials fail, usually because of unanticipated side effects.

The problem is no surprise to Dr. Schadt. “It turns out that common diseases involve thousands of genes and proteins interacting on complex pathways,” he said.

In 2003, Dr. Schadt was first noticed as a co-author of a paper in Nature that articulated the need to move beyond the impact of individual genes on disease and to create computer models of diseases that included the interaction of genes and proteins.


Here in lies the debate between the SENS approach and the evolutionary/genetic approach to not only curing disease but ultimately reversing aging. Metabolism and the genetic pathways that create diseases (cause damage) are extraordinarily complex. The end damage is a more easily understood target. Dr. Rose says that genomic manipulation is like nuclear fusion while the SENS-damage approach is like playing with fire. That may well be, but if playing with fire can saves some lives up until the time (could be a long time) we can safely manipulate metabolic pathways with skill, then it is certainly worth pursuing.




0 user(s) are reading this topic

0 members, 0 guests, 0 anonymous users