La Folie, Quo Vadis, Evo-Devo?

tYNA
http://tyna.gersteinlab.org/tyna/
可以download一些已經建好的network
 

http://biit.cs.ut.ee/mem/
MEM - Multi Experiment Matrix
Given a gene as an input, MEM ranks other genes by their similarity in
each individual data set.

Optimization in MATLAB
http://www.iim.csic.es/~dotcvpsb/

http://gaggle.systemsbiology.net/docs/
GAGGLE
整合用軟體   看起來頗強大

http://www.broadinstitute.org/scientific-community/software
Scientists in the Broad community have developed many critical software
tools for the analysis of increasingly large genome-related datasets,
and they make these tools openly available to the scientific community.
For the conditions governing the use of Broad Institute software,
please see the software use agreement associated with the tools you
choose to download.

http://www.snp-nexus.org/index.html
SNPnexus database is designed to simplify and assist in the
selection of functionally relevant Single Nucleotide Polymorphisms
(SNP) for large-scale genotyping studies of multifactorial disorders.
SNPnexus allows single or batch queries using dbSNP identifiers
or in-house SNPs genomic coordinates on clones, contigs or chromosomes.
SNPnexus will be updated on a regular monthly basis and will provide
the scientific community with a common friendly web-
interface to perform the following analyses:

http://seqanswers.com/wiki/Software/list
https://wiki.nbic.nl/index.php/Next_Generation_Sequencing:_Software
各種sequence analysis相關的軟體

http://sites.google.com/site/nextgengenomics/ingap
inGAP is an integrated platform for
next-generation sequencing project, the core function of which is to
detect SNPs and indels using a Bayesian algorithm.
(1) It does not
have any read length restriction. It can handle 454 sequencing and/or
Illumina Solexa sequencing and/or Sanger sequencing data sets.
(2)
It can detect most small indels in either single-end or paired-end data
sets. Using the simulated data sets, inGAP could successfully identify
85%-98% of small indels with high accuracy (>99%).
(3) It has a
strong capability to identify variants based on a relatively divergent
reference genome, which bring it to a much wider application other than
resequencing projects.
(4) It provides a user-friendly graphic
interface, through which users can browse, search, check, classify, and
even edit the identified variants.
(5) It can be used to detect
intraspecific polymorphisms (including SNPs and indels) based on a
pairwise comparison of multiple whole genomes.
(6) It employs a global heuristic searching approach to layout contigs based on one or more reference genomes.
(7) It also provides a handful of bioinformatic tools for read simulation, mutation incorporation, format conversion, etc.
(8) inGAP-sv (structural variation detection) will come soon.
•    Installation
inGAP is distributed under the GNU General Public License. The latest version can be downloaded at http://sourceforge.net/projects/ingap/
.
inGAP has been tested on PC, Mac, and Linux systems. To install InGap, type the following commands.
% tar xvfz inGAP_*.tar.gz

•    Demo
We provide a demo for the three applications of inGAP. Please click the "Demo" button.
•    Getting started
1.    Double click the icon “inGAP” at inGAP_HOME or start it from a command line:
% inGAP_HOME/inGAP
or
% java -mx2000m -jar inGAP_HOME/inGAP.jar
Then you will see the following panel:

Dear GSA members,
At the outset of a new academic year, the TIGP Administration Office wish to express our best wishes for your academic progress and overall fitness.
I have a special affection for those of you who is about to or has just joined a research group and start your these project. On the other hand, I sincerely hope that all senior students are enjoying more than suffering from their research activities. While the sea appears to be calm, we know there are many prey-predator competitions going on in the waters. While there’s little I can do to improve your swimimg skills, I think knowing other players in your ecosystem better should increase your chance of survival and live happier.
Attached are several short articles that I came across at websites that teach graduate students-to-be "survival skills", while your are already in this puddle I believe these articles (and others you may find at the source website) should still help you reflect your situation and make necessary adjustments to your everyday survial strategy.
Overlayed with these generic survial struggles are cultural differences that some of you may consider it imposing unfair treatments on foreign students. Should anything bothers you or hampers your academic progress that you cannot resolve by yourself, please see your Student Affairs Advisor in your program, or contact me through phone or e-mail for an appointment so that we can chat cosily in an trusting environemnt.
Wish you all flourish and pleasant,
Sincerely yours,