The conceptual framework of Galaxy is truly attractive for non-programmer experimental biologist like me.
I was wondering if there is a similar platform for microarray analysis?
Hello Jean-Philippe,
http://chipster.csc.fi/ has microarray tools based on Bioconductor packages like Limma and friends that may suit some of your needs. I believe a VM image is available to simplify installation if you want to try it out painlessly.
Virtual machine (VM) image is a set of files that contains a complete system, such as Chipster. It includes the operating system and required software. VM images are run with virtualisation software, such as VMware Player or VirtualBox for normal laptops, or OpenStack for powerful clusters. Virtual machines save you the hassle of setting up a physical server.
There are different kinds of VM images. Some contain only the essentials and require the user to install analysis tools and reference data, while some are complete and ready to run analysis tasks. The Chipster VM image belongs to the latter category, containing a wide selection of analysis tools and reference genomes. Of course this means larger downloads initially, but less tweaking later on.
Thank you!
Please review the other Public servers available for one option (these update frequently). Search on the wiki for "microarray" to start with:
http://wiki.galaxyproject.org/PublicGalaxyServers
Some of those tools may be in the ToolShed for local/cloud use, permitting you to scale up dedicated resources as needed:
http://usegalaxy.org/
http://usegalaxy.org/toolshed
http://wiki.galaxyproject.org/BigPicture/Choices
And if you have programming experience or resource where you are working, almost any tool your prefer could be wrapped and added to use within Galaxy. (And please consider sharing, contributions to the ToolShed are always welcomed!):
http://wiki.galaxyproject.org/Admin
http://wiki.galaxyproject.org/Admin/Tools
Best, Jen, Galaxy team
Hi Jean-Philippe,
Like mentioned in the previous answer, Chipster is available as a VM image which contains all the analysis tools and reference data. Note that we offer evaluation accounts to our Chipster server, as people often want to try the software before downloading it (the VM is quite large because of all the aligner index files etc).
Best, Eija, Chipster team
Thanks alot for your quick answer.
Sounds like chipster required a significant amount of R programming and is not free.
Any other options?
Jean-Philippe
Hi, Jean-Philippe.
I don't actually use it, but I'm pretty sure Chipster is open source - at least http://chipster.github.io/chipster/ confirms that but the chipster team can tell us what the real deal is!
I have also heard of people using genomespace (free - from the Broad) and non-free options including CLC Bio and Partek for microarray analysis. Asking this Galaxy group (most of whom have to some extent "voted with their feet" and so don't make much use of closed source and other options) might limit the extent of our collective expertise to help. Perhaps a more general forum such as the general Biostar forum or seqanswers might get a wider range of readers than this Galaxy sub-forum for your enquiry?
Hi Jean-Philippe,
Sorry for not being more specific, Chipster is often confused with commercial software but it is open source like the previous answer already said. So you can download the VM and set up your own server free of charge. If you want to run Chipster on our server in Finland permanently, we have to charge for computing time. This is because our computing center is owned by the Ministry of Education and the funding supports only Finnish universities. Anyhow, we are allowed to open free evaluation accounts if you want to try Chipster first.
You don't need any R (or other) programming experience to use Chipster. It has been developed especially for non-programming wet lab scientists, as this is our largest user group (we are the national bioinformatics core facility in Finland).
Best, Eija, Chipster team
