Hi, I am in the process of defining a baseline server for bioinformatics analysis of next gen data. I am not going to be the administrator of this machine so here is the list I came up with for the initial configuration. This machine is going to be used for post alignment and variant calling steps but it would also be nice to have that capacity as well. What other software packages and tools or modifications do you think is necessary for a good bioinformatics server?
Linux OS Apache Server Php MySql PostgreSQL >optional but I suspect we may need it in the near future Perl Python 2.6x , 3.1 R Bioperl, biopython and bioconductor for R can be installed by us or for us
Media wiki installation > we can do this install or we need to be able to have full access to its administration
Access to apache configuration Admin rights for mysql database
Ports: SSH, 80 for intranet
then read this article: http://www.nature.com/news/2010/100428/full/4641260a.html (Cybersecurity: how safe is your data? from NatureNews)
do you mean a web server, or a service server, e.g. a place where users can login to do their analysis
both. but more a web server since we already have service servers that we have access to to do our own analysis with scripts etc. but we want to make the analysis results available to the end user mainly as data table, search and filter etc. functions. but we also want to be able to make some analysis as well.