Clinical & Translational Science Center

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Bioinformatics & Computational Biology

Weill Cornell Medical College Institute for Computational Biomedicine (ICB)

Faculty and Staff of the Institute for Computational Biomedicine are available for consultation and collaborative projects in all areas of bioinformatics. Specific translational bioinformatics support is offered through the biomedical informatics key function of the CTSC. It mainly focuses on the development of new computational methods and tools to facilitate new biological discoveries, especially for the analysis of high-throughput datasets (e.g., measurements of gene expression, genetic polymorphisms, protein levels, or epigenetic modifications).

For questions about translational bioinformatics, please contact Dr. Oliver Elemento. For questions about computational methods/tools, please contact Manuele Simi.

The MetaR software is a new kind of interactive tool for data analysis. It was developed by using the Meta Programming System (MPS), a mature Language Workbench to create new languages and tools to help users of these languages. 

MetaR is designed to make it easier to conduct data analysis. To achieve this goal, and in contrast to programming languages such as the R language, Julia or Python, that are often low -level and require good programming skills, MetaR offers high-level data abstractions and provides assistance in manipulating data. High-level abstractions used in MetaR analyses include the following concepts:

  1. Tables, Columns, Column Groups and Group usages
  2. Analyses
  3. Plots
  4. Models 

Analyses developed with MetaR are transformed into R programs when the user needs to execute them. MetaR is tightly integrated with MPS to make it seamless to run analyses without prior knowledge of the R language. An Integrated Development Environment is distributed with MetaR to provide a single program in which all development and executions are done. 

Starting with version 1.3.1, MetaR can optionally run the R scripts that it generates into Docker containers (again, no prior knowledge of Docker is required), a technology that makes it easier to obtain reproducible script executions. 

For questions about MetaR, please contact Manuele Simi.

Click here to register for MetaR training session.

MSKCC Bioinformatics Core facility (BIC)

Personnel from the MSKCC Bioinformatics Core (BIC) perform scientific and technical consultations on a wide variety of bioinformatics topics. For example, topics have included, but are far from limited to, expression (mRNA and miRNA) microarray differential analyses, data mining of public and in-house gene expression data, normalization and segmentation of array CGH and SNP data, sequence assembly, mapping and variant detection, sequence data processing and extraction, selection of genes based on public annotations, and motif detection in DNA and protein sequences. BIC personnel have consistently focused on providing data processing and analysis services (either from computational tools developed internally or acquired externally), evaluating results for statistical significance and placing the data in context of the wider body of available biomedical data. There is a fee for these consultation services, which is based on an hourly rate or fee based on the amount and type of data. Price estimates are available after an initial consultation.

For more information about the MSKCC Bioinformatics Core, please contact Nicholas D. Socci, PhD.

Clinical & Translational Science Center 1300 York Ave., Box 149 New York, NY 10065