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Bioinformatics Resources at Penn: Our Services

This guide provides patrons with a list of Bioinformatics resources available across the University and by the Penn Libraries

Overview of Services

The Penn Libraries’ Holman Biotech Commons is stepping up efforts in supporting bioinformatics needs across the Penn campus. While we already provide access to bioinformatics-specific books, e-books and journals, and there are several Research Cores (e.g. BIC, ITMAT) that support high-end bioinformatics needs, at the Holman Biotech Commons's our focus is on filling gaps in those existing services.

Learning and Training Assistance

Our staff provides one-on-one consultations, workshops and webinars to get you started using bioinformatics databases and tools such as:

  • NCBI. This resource provides access to dozens of data repositories, tools and reference materials, with Pubmed being the most heavily used. We provide assistance with those NCBI resources more closely related to bioinformatics, for example:
    • Basic Local Alignment Search Tool (BLAST) – Tool to find regions of similarity between nucleotide or protein sequences.
    • Gene – Portal serving data centered around a specific gene.
    • ClinVar – archive of reports of the relationships among human variations and phenotypes, with supporting evidence
    • MedGen – portal to information about human disorders and other phenotypes having a genetic component. 
    • Cn3D – 3D viewer that displays structure, sequence, and alignment, and also includes annotation and alignment editing features.
  • Cytoscape- An open source software used for visualizing networks of molecular interaction and biological pathways.
  • BioCyc Database Collection- BioCyc is comprised of 14560 Pathway/Genome Databases (PGDBs), and tools for exploring them. It provides electronic reference sources on the pathways and genomes of many organisms. In addition to the databases on the model organisms such as yeast, fly, and mouse, BioCyc also contains databases for humans and for other eukaryotes whose PGDBs have been curated.
  • Repbase- Repbase is a database of prototypic sequences representing repetitive DNA from different eukaryotic species. Repbase is being used in genome sequencing projects worldwide as a reference collection for masking and annotation of repetitive DNA (e.g. by RepeatMasker or CENSOR).

We also support Data Visualization needs through:

  • Data Visualization basics workshop: An overview of the What and the Why questions around visualizing data, broadly, as well as guidelines for best practices.
  • Consultations on effectively displaying your data for publications or presentations.

Research project assistance

We can offer answers to basic questions on:

However, we can’t:

  • Clean your data
  • Analyze your data
  • Create figures or any other visualizations

For these services, we refer you to the Bioinformatics’ cores mentioned in the following tabs (pages).

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