Tools
Microarray analysis Packages: Support to design and run microarray experiments can be obtained from the Microarray Core facility. Support to design microarray experiments and analyze data can be obtained by contacting John Tobias in the Bioinformatics Core. The Bioinformatics Core in collaboration with the Penn and CHOP Microarray Core Facilities, has negotiated licenses for GeneSpring, Partek, Ingenuity and Spotfire. Click here for additional information about microarray analysis support and tools and how to sign up for this service.
Desktop Sequence Analysis Packages: The Bioinformatics core facility has set up keyservers to provide cost effective access to a variety of commercial desktop packages that run on Windows or Macintosh computers including MacVector, Sequencher and Lasergene. Click here for additional information about these packages and how to sign up for this service.
UNIX tools: A variety of UNIX based tools will be made available as needed. Programs currently installed include BLAST (WashU and NCBI), BLAT, FASTA, SIM4, EPCR, RepeatMasker, PHRAP/PHRED/CONSED, polyphred, GeneHumter2 and the EMBOSS package which contains programs for sequence analysis including protein structure prediction, pattern matching, phylogenetic reconstruction, mapping and many others. See below for information on requesting an account.
Liniac Compute Cluster: The Genomics Institute and Bioinformatics Core also support a large parallel compute cluster (currently 256 processors) for large compute intensive jobs. Information about the liniac cluster can be obtained from the liniac home page. The "Users" link is particularly relevant when getting started using the system. Documentation specific to using genomics applications can be found here. Logins to utilize the liniac can be obtained by sending email to the bioinformatics core facility requesting an account and indicating your use for such a resource.
iNquiry: iNquiry is currently down. Please contact us for help in identifying alternative resources or for more information on the status of this service.
GCG: GCG is no longer supported by the Bioinformatics Core. Please contact us if you need help moving data from your GCG directories to another machine.
Requesting Accounts: Requests for accounts to access the UNIX compute servers can be made by sending email to the bioinformatics core facility. Please include your full name, Penn phone number and Penn ID number in your email.