Software, database and website development

The core offers software, database and website development for basic research and clinical research.  Managing, storing and querying data is an integral part of research.  The way data is stored and accessed often defines the efficiency of the research process.  The Bioinformatics Facility addresses this challenge by designing and hosting Laboratory Information Management Systems (LIMS), including: (1) designing database systems for specific research problems; (2) developing interfaces for data access, storage and analysis; and (3) deploying these applications on the core’s computing resources. 

Examples of this type of service include:

  • Plant Proteome Database (PPDB) for Arabidopsis thaliana and maize (Zea mays).  PPDB is both a LIMS and a public outreach/publication tool.  Data access level depends on login credentials.  (This application was developed in collaboration with Klass Van Wijk at Cornell University.) 
  • PathogenTracker is a web-based tool and LIMS for studies on bacterial biodiversity and strain diversity.  (This database was developed in collaboration with Kathryn Boor and Martin Wiedmann at Cornell University.) 
  • Panzea Database contains the genotypic and phenotypic data and genetic marker information produced by the NSF-funded project, “Genetic Architecture of Maize and Teosinte.”  (This application was developed in collaboration with Ed Buckler at Cornell University and the USDA-ARS.) 
  • Hepatitis C Datamart LIMS integrates clinical data (hospital databases), local biomedical research group data,  genotyping and tissue/sample bank data in support of medical research.   The Bioinformatics Facility designed the database schema, developed a web based LIMS, and currently manages the database.  The Datamart LIMS is compliant with patient data privacy regulations and allows physicians to use this system for integrating various EMR data. Datamart is capable of importing and analyzing data from different sources (hospital databases, EMRs, local research databases). The LIMS is now designed in such a way that can be easily adapted to serve needs of diverse research groups since it can be customized by the end user without need of any programming or code development.  (This database was developed in collaboration with Andrew Talal at the Weill Cornell Medical College.)
  • T-REX is an online tool for storage, management, and analysis of Terminal Restriction Fragment Length Polymorphism (T-RFLP) data.  The interface allows for uploading, storage and analysis of T-RFLP data and can be used as a LIMS.  It is an example of online hosting of algorithms and software developed at Cornell.  (This application was developed in collaboration with Steve Culman and Dan Buckley at Cornell University.)