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Bioinformatics Resources

We are constantly evaluating our users’ needs to ensure that they have the bioinformatics resources they need to conduct their research.  If there is software or analysis tools that you need, please let us know so that we may set them up for you.  Tools currently available or soon to be available include:

Gene Expression Analysis Pipelines

Pipelines for RNA-Seq, ChIP-Seq, and related processes are currently under construction.  Our goal is to make these pipelines flexible to allow for customization of analysis.  If these tools will be useful to you or if you have a preferred analysis method that you would like us to implement, please contact us for a consultation.

Genome Assembly Pipelines

We can help you assemble genomic read data from next-gen sequencing pipelines, including assembly to a reference genome or de novo assembly.

Molecular Modeling

The Bioinformatics Core utilizes numerous programs for modeling and analysis of protein structures.  The software we utilize includes Discovery Studio, AutoDock, Chimera, and others.  Possible analyses include homology modeling, docking analysis, etc.  Many of these programs are only available locally at URI on our Core machines, but we are planning to migrate them to our server to allow for off-site access.  We are also evaluating demand for Biovia’s Discovery Studio which is part of the Pipeline Pilot suite of software.  If you are interested in using Discovery Studio or associated software, please contact us.

Adobe Creative Cloud

The Bioinformatics Core maintains a team license to the Adobe Creative Cloud software that includes Photoshop, Illustrator, Premiere Pro, etc.  INBRE researchers who need short-term use of  this software may request access to a “seat” (ie an individual license administered by the Core).  Researchers who need long-term access may purchase a seat under the Core’s team license.  Please contact us for details.

Bioinformatics Listserv

To simplify communication and keep our users up to date on Core functions, we have set up a listserv at URI.  To join the listserv, send an email to listserv@listserv.uri.edu with the following in the body of the message: subscribe INBRE-BIOINFO your name

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