Can anyone suggest am alternative to SDSC biology workbench? Either open source or cheap license?

Dear Rasika,

I assume you are looking for a "point-and-click" user interface as opposed to environments like Bioconductor, Biopython or Biopieces where you have to work on the command line mostly.

In a way, Taverna (http://www.taverna.org.uk/) and Galaxy (https://usegalaxy.org/) may be good replacements. They are both powerful "workflow management tools" with some kind of graphical user interface, but perhaps not as easy to use as The SDSC Biology Workbench.

If you need something simple and don't mind copying and pasting data via the clipboard, the Sequence Manipulation Site (http://bioinformatics.org/sms2/about.html) and EBI Services web collection (https://www.ebi.ac.uk/services) could be useful.

Invest on local infrastructure - can be started with simple 1 computer - Biolinux with

1) use python, bioconda https://bioconda.github.io/

2) use R + bioconductor

and combine with open source tools like

EBI Services web tools - https://www.ebi.ac.uk/services

Galaxy - https://usegalaxy.org/

MPI Bioinformatics toolkit - https://toolkit.tuebingen.mpg.de/#/

NCBI Genome Workbench -https://www.ncbi.nlm.nih.gov/tools/gbench/

Sequence Manipulation Site - http://bioinformatics.org/sms2/about.html

Taverna - http://www.taverna.org.uk/

UGENE - http://ugene.net/

Thank you for both of your suggestions. I tried the Genome workbench. It is a learning curve and I am still at the very beginning. But I am getting the hang of it. Thank you to both of you.

I think most or all tools in the SDSC Biology Workbench are individually freely available, but I'm not aware of a similar server environment with all the tools and a user account for storing data/results. If you are still looking for the basic tools at one site, I recommend ENSEMBL-EBI: https://www.ebi.ac.uk/services

For beginners try DNA Subway: https://dnasubway.cyverse.org/