Good afternoon,
I wonder if anyone has had positive experiences with any open-source pathway analysis programs? I am looking for something more than Netaffx for my Affymetrix data. The free trial of Ingenuity Systems' pathway analysis software founded on a hand-curated database has been very impressive, but the software is really expensive.
Comments
more on pathways
Interesting comments, some of the commercial pathway analysis tools are indeed quite good. I'm also working on a pathway-based analysis of genotype data, the paper is in press in the Journal of Biomedical Informatics and the tool will be made publicly available soon. valentin dinu, http://www.dinuinformatics.info
Pathway analysys and discovery
It's an old discussion but it still comes out on google search...
I was recently trying to find good pathway analysis software (preferably free), reviews or anything. What I found interesting is DAVID, which is not really pathway analysis soft but quite useful tool anyway, and Pathway Discovery site with some great tips. Hope this helps.
Ingenuity Pathways Analysis
Have you tried the new ingenuity Pathways Analysis 3.0 ? You can get a new free trial. I am ready to bet that this one is going to make it big time.
this post sponsored by...
...it's easy to spot posts from people promoting companies, you know :)
Our original poster specified an open source solution - I think he wants it to work for longer than 30 days.
Check out cytoscape
Cytoscape (www.cytoscape.org) is an open source network analysis workbench. The raw program doesn't know anything about biological analyses, but you can download and install all kinds of cool plug-ins (see website) that do specific tasks.
I can recommend
I can recommend Pathway Assist. IMHO this is a cutting-edge product and shows where things can/should go in the future. There are many things to improve, performance for example. Nevertheless, the program opens you a whole new look at literature and networks/pathways. The data is derived from PubMed by literature mining. Quality of the networks is surprisingly good.
Open-source software, on the other hand, is lagging behind. Projects like Biocarta, GenMAPP etc. are really great. However they only provide static snapshots of pathways ("cartoons"). You can not interactively work with the software to explore the pathways behind.
rule based approach
http://www.genepath.org/
Open-source pathway analysis
It sort of depends on what exactly you want the software to do, but there's a free package called GenMAPP that allows one to map the results of array experiments onto known pathways. There are lots of pre-existing templates for known pathways and the opportunity to enter your own if you like:
http://www.genmapp.org
Hope that helps.
> Good afternoon,
>
> I wonder if anyone has had positive experiences with any open-source pathway
> analysis programs? I am looking for something more than Netaffx for my
> Affymetrix data. The free trial of Ingenuity Systems' pathway analysis
> software founded on a hand-curated database has been very impressive, but the
> software is really expensive.
accelerating pathway analysis
You may want to take a look at the product below, if you are using open source analytics tools, TB will help you build a worflow and execute them in an distributed environment...company is called turboworx
i hope this helps
TurboWorx Builder