Slashdot Mirror
Open-Source Bioinformatics Programs?
An anonymous reader asks: "This summer I have the opportunity to work in a bio research lab creating a web site for data about proteins. Part of my job is to do bioinformatic analysis of the proteins to determine what types of support their are for the preliminary gene predictions. I have been using DNA Stryder (a Mac program) for sequence alignments plus translations from DNA sequences to protein sequences, and I was wondering if any of the Slashdot crowd knew of similar programs for Linux? I have looked into Bioperl , Biopython, EMBOSS, and BioConductor, but they seem to be more oriented towards servers and less towards stand-alone applications. What programs would you suggest, especially those that might be geared more towards biologists rather than computer scientists?"
I'm working on something to do basic sequence analysis in my spare time right now.
I'm not a bio researcher, but I am a programmer and I work in the field. My father is a biology researcher and we've been talking about putting together a GUI app that interfaces with various tools to provide an easy interface to common tasks that bio researchers have: basecalling, vectormasking, clustering, sequence alignment, along with a nice GUI that lets you play with the results (search the results, order them, associate them with different databaes, relate them to gene ontologies - essentially a powerful set of data visualization tools).
It's all focused around EST management. Our goal is to get an app that a non-power-user can get up and running, out-of-the-box, for managing small sets of libraries.
It's pretty obvious that there are a very solid set of OSS base tools that implement the algorithms for doing analysis on ESTs, but in terms of glue apps that bring all of the tools together into a cohesive whole, there's not much out there.
What IS out there is hopelessly complex to expect an average bio researcher with little time on his hands to get up to speed with ("Download and install mysql? wtf?").
The problem is that most of these tools are geared towards large institutions with dedicated bioinformatics departments. They have the resources to hire a couple sysadmins and programmers and set up a high-throughput management system. Most small-timers don't really have the resources to get these apps working. I want to write something targeted specifically to smaller labs.
I just started writing it last weekend.. so it's not like there's much there yet - OTOH I have programmed a high-throughput EST management system for my work, so I have a good idea of most of the design issues.
An OSS app in this area would rock. It's a great opportunity to add to the wealth of OSS tools in the field, and I think it would solve a real need.
If you want to talk about it, reply to this post and also send me a message kav062 at yahoo dot com.
-Laxitive
My company, CLC bio, just released a free bioinformatics application that works for Linux, Mac and Windows (not open source). It was designed with molecular biologists and biochemists in mind, rather than bioinformaticists. Thus, a lot of effort has been put into the user interface.
The program is a 0.9 beta and so far it only has basic functionality: GenBank searching, DNA/RNA to protein translation, alignment, tree reconstruction, graphical viewers, and a few other things. More will follow in the coming months.
Thanks,
Bjarne