Organism portal framework

Question

[hbw]

I want to put up a portal for my relatively obscure organism. I will have my own genome, some gene annotations, some gene expression (RNA-seq) results, perhaps some proteomics data. The project does not justify a full time web developer. I am looking for some software which will let me host this in a friendly fashion once I give it my files in some suitable format. I know I can use gbrowse to host the genome sequence. How can I get all the data to play nice with each other, so that clicking on a gene will lead can get us to the locus on gbrowse, its GO annotations, BLAST results, diff expression results, etc. Instead of re-inventing the wheel shouldn't we be able to get a stripped down version of http://www.informatics.jax.org/, http://www.yeastgenome.org/, or https://www.arabidopsis.org/?

[Michael]

See also: What Is Your Experience With Gmod Tools Or Alternatives?

Answer 1

[Neilfws]

You may want to investigate Tripal (also published), a genome portal solution based on the Drupal content management system.

There was a similar older project based on Turnkey, but I'm not sure that it is maintained any more.

[Adamc]

Do you happen to know of anything similar but geared more for expression datasets? Microarray and/or RNA-Seq. Don't want to re-invent the wheel if it's not explicitly necessary.

[Michael]

Agreed, Tripal provides

"so that clicking on a gene will lead can get us to the"

• locus on gbrowse (minimal coding, put a link in the feature template)
• its GO annotations (no coding)
• BLAST results (no coding), can also run new Blast jobs
• diff expression results (minimal coding or linking to existing scripts)

Answer 2

[Pierre Lindenbaum]

You could host all your files on a public server and just set up an UCSC Assembly hub? https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser

or a Genome Browser In a box: http://genome.ucsc.edu/goldenPath/help/gbib.html

Genome Browser in a Box (GBiB) is a "virtual machine" of the entire UCSC Genome Browser website that is designed to run on most PCs (Windows, Mac OSX or Linux). GBiB allows you to access much of the UCSC Genome Browser's functionality from the comfort of your own computer. It is particularly directed at individuals who want to use the Genome Browser toolset to view protected data.

Answer 3

[hbw]

Caleydo seems to be geared towards pathway analysis.