2. Bioinformatics services
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a. Emboss and wEmboss:
Access to Emboss software is available on server, which provides both shell and web access. In both cases you will need an account. You may request an account here. The server hardware is a single quad core 64 bit host with 4 gig of ram.
For shell access to command line tools:
> ssh -Y emboss.uit.tufts.edu
For access to the web interface wEmboss.
For access to emboss web documentation.
Former GCG/Seqweb users can find equivalent Emboss functionality
here:
Emboss tutorial
If you have any questions about Emboss related usage, applications, or assistance with software, please contact bio-support@tufts.edu.
Bioinformatic related FAQs
Where are my old seqweb sequences:
Your old seqweb data is at: /nfshome/seqweb/users/your-user-name/
There you will find three directories with your data:
result state work
You may retrieve these with a file transfer program like
WinScp (http://(www.winscp.org) and store locally on your pc/mac. You may then
use a local web browser to look at the old seqweb data. You may also cut and paste sequence data into a wEmboss web session.
If I use the web interface to emboss where is data stored:
wemboss data is written into a directory called wProjects under your shell account. The path will be: /home/your-user-name/wProjects/
Will I have access to my old gcg shell account and data:
Your home directory on the old bioinformatic server is mounted as your directory on the new emboss server. However, access is via a shell login, not with the web interface, wEmboss.
b. Carmaweb server (please click on link)
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UIT and the Medical School hosts and supports a web based service known as CarmaWeb. The focus of CarmaWeb is genetic microarray analysis. CARMAweb is a web based tool that allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. These tools are built upon bioConductor and R software. One may request an account via the website.
Additional information here.
A CARMAweb tutorial is available here
The server hardware is a single quad core 64 bit host with 4 gig of ram.
If you have any questions about CarmaWeb related usage, applications, or assistance with software, please contact bio-support@tufts.edu.