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Custom software development

The Center for Computational Biology has wide ranging experience in creating custom scientific software. Projects for researchers at Scripps include:

  • HDX MS data analysis
  • ImageJ plugins to automate region of interest mapping and particle analysis
  • Visualization of sequence data using BioJava
  • Automated sifting and aggregation of 100’s of Graphpad Prism worksheets
  • Automated searching and report generation from Biological websites e.g. CREB database, Facility animal management database
  • Use of Lilly MedChem Rules chemical descriptors
  • Automation of multi-plate export from Cellomics CellInsight system
  • Excel calculation templates for mouse metabolism studies, %Inhibition calculation, well mapping etc.
  • Excel Addins for image management, NCBI Entrez / PubMed interation, etc.
  • Web-based microarray and RNA-Seq data processing and visualization tools

We would be pleased to discuss these types of projects in context with your research interests. Many problems can become more tractable by utilizing simple software tools.


  • Bruce Pascal, Bioinformatics Project Manager, Publications