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Bioinformatics Help

Suzy Strickler (Mueller lab)

Suzy Strickler (Mueller lab) tracks requests and sets up help with bioinformatics analyses and training. Yi Zheng (Fei lab) also provides consulting, training, and backup.

As a follow up to Boyce Thompson Institute’s (BTI’s) Strategic Plan that was formulated around bioinformatics core support, BTI is sponsoring free consulting for all BTI researchers.

What Is Bioinformatics?

Bioinformatics aims to address biological questions and problems by using and/or developing computational tools. Large amounts of data are now being generated through various “omics” methods that can collect data from entire genomes, transcriptomes, proteomes, and metabolomes. Bioinformatics tools are critical in mining these data and deriving meaningful, biologically relevant conclusions. Bioinformatics relies on a well-developed infrastructure for software, data storage, organization, and access. To provide for this, a number of biological databases exist for a variety of purposes. For example, databases currently exist that compile the massive data output from genome projects, pathogen sequences, gene families, and so forth.

BTI Servers William and Boyce

The bioinformatics team has installed a new server, called “William.” It runs Ubuntu Server Linux and has 128 GB of RAM, 64 cores, and 6 TB of disk. It is suited to run smaller jobs, such as BLAST and NGS read mapping, that do not require the power of “Boyce,” the large memory machine. The Boyce server is designed to run larger jobs. If staff plan to run smaller jobs, they may want to request an account on this new William system, to free up Boyce for the larger tasks. All BTI staff are welcome to use the new server at no cost. Staff are encouraged to schedule their use of either server using Google Calendar. Suzy Strickler can facilitate access and explain how to use the calendar to make reservations. Learn more about the servers and reservations on this page.

Services

Assistance with basic tools and software installation, assistance with Linux, differential expression analysis for RNA-seq data, SNP-calling, and other analyses.

Experimental Design

Bioinformatics consultants can help with experimental design to maximize the value of results.

Education

In addition to the bioinformatics courses already offered through the Mueller lab, feedback will be solicited to enable the design of web portals and/or short courses illustrating best practices dealing with most commonly used analysis pipelines.

Bioinformatics Practitioners Club

Seminars are typically organized once a month during the fall and spring semesters in Weill Hall (Room 221 or 321). If interested in participating, simply come to a session, and make sure to subscribe to the mailing list: http://rubisco.sgn.cornell.edu/cgi-bin/mailman/listinfo/bti-perl-club. Contact Surya Saha if you have any questions. For more information visit http://bti-perl-club.blogspot.com/.

Contacts

Susan Strickler (Mueller lab) will be the primary point of contact for BTI Consulting. She will track requests and help to establish the appropriate contacts for analyses and training, depending on the expertise that is required. Yi Zheng (Fei lab) will provide consulting and serve as backup when Suzy is unavailable.

Office Hours

A new Bioinformatics Consulting Space has been created in the resource center on the second floor. Consulting requests should be made by: 1) visiting during the open office hour Wednesday 12pm, or 2) e-mail contact. Please restrict your requests to these two mechanisms to allow the consultants to pursue scheduled consulting work as well as their own research.

Bioinformatics is commonly used for:

  • Genome Assembly
  • Genome Annotation
  • Comparative Genomics
  • Gene Family Analysis
  • Expression Analysis Using RNA-seq
  • Network Analysis

Some example of biological databases:

For more information please contact Susan Strickler.