Sunday, March 25, 2007

Bioinformatics Infrastructure

1. LIMS
I have already listed in a post before

2. Web Interface for customize Program release
We need a web system to allow biologist to access the program we develop through a Web interface. This is to avoid programer to install on different platform. The advanges is that the program can be used easily by other people.
Most of the programs in this category will need input file from users and get result back.
Things need to be done:
a. Web interface
b. Backend data processing
c. Privacy protection.

PISE package is a good starting point: http://www.pasteur.fr/recherche/unites/sis/Pise/

3. Computation Pipelines
a. EST Clustering and analysis
b. Sequence calling and assembly (Phred/Phrap/Consid)
c. Association Studies
d. Data Integration (iProtein)
e. Network and Pathway analysis
f. Structure prediciton and modelling
g. Data submition to public databases (NCBI, PDB, GEO)
h. SNP analysis
i. Workflow (Keppler)

4. Local databases
a. NCBI
b. SRS
c. Human Genome Browser

5. Software tools
a. GeneString (microarray analysis)
b. Spotfire (Multi-dimentional data analysis and visualization)
c. Matlab
d. Mathmatica

6. Project managment tools, Time Management and tracking, CRM

7. Cluster Computing Infrastructure
a. open source software in cluster environment (some of them from ROCK distribution)
b. local databases

8. Computing infrastructure

a. Servers
b. Development environment (Test, Develop, production environment)

9. IT infrastructure
a. Network (DNS, DHCP)
b. Security (Kerberos, Firewall)

1 comment:

Chris said...

We've been using STARLIMS Lab Management Systems because all our labs perform critical and complex processes that require total regulatory compliance. We found through research that STARLIMS is the most effective web based LIMS Software