| | Re: Your set of bio-info tools and why it's great :)
Ohh wrong Button pushed...
I like Geneoius because its easy to handle and manipulation and overwiewing lots of data (Primer Creation) is quite fast. Okay next one:
Primer Blast(Web-based on NCBI): Allows of quick Specifity check, but it doesn't allow max 5' Stability settings, so I don't prefer it for Primer Creation.
Oligo Explorer: A bit old and doesn't support melting temperature calculation after Santa Lucia, but has the great possibility to control Primer-Dimer and Hairpins directly visual (Alignment scores got not an absolute evidence) and calculates (after Breslauer et. al) the melting temperatures of Dimer/Hairpin structures.
Copasi: Great tool for analyzing biochemichal networks. Provides both, stochastical Calculations and deterministic calculations based on differential equation. Ist one of the seldom all in one analyzing and simulation tools for systems biology.
Celldesigner: A biochemical network visualization and analysing/simulation tool. Can be used with Copasi together (seperate or through SBW).
Cytoscape: Primary used as visualization tool. Highly modifyable through plugins. Very good visualization possibilities.
Not direct tools, but support software:
SBML(systems biology markup language): Hope this will be the total standard in nearest future, so theres no need for so many conversions for different filetypes (some are just for visualization, some are just for kinetis equations,...) because in SBML theres all in one.
SBW(Systems biology Workbech): Creates good Connectivity between different programs (like Copasi and Celldesigner), so there is a good workflow guaranteed.
R and Rapid Miner should be mentioned, but I'm not sure, if they belong here.
I think it's enough for the first time. Maybe I got another idea later...