January 3, 2012

Bioinformatics

Our quantitative and computational analytical unit sits at the cutting edge of bioinformatics research — we use the latest tools and develop improvements to correct short comings with these tools. In addition to providing you the best bioinformatics service and data support, we strive to be the a premier services facility in terms of applied bioinformatics methodology research.

Working with Bioinformatics Scientists: Our engagements begins with an investigator contacting TxGen’s Director to set up a meeting and discuss their research program and desired research project. Once all the details are worked out, a scope of work/quote is prepared, which describes the work to be performed, defines deliverable, project costs, and sets timetables for laboratory and/or bioinformatics. Most bioinformatic services are performed on a fee for service basis, for each project a service quote will be generated and approved by the PI before any work is begun. Primary base calling, QC. and processing of sequence data to fastQ format is provided at no cost. Once a project is completed it is then presented to the investigator. From there our services continue as we provide software and human insights into their projects and help them take the next steps; publications, grants, follow up studies, etc.  

Internal Development: We have launched a Dynamic Technology Development and Adaptation Program where new technologies are brought in and/or established, ensuring that we remain a leading genomics facility. The breadth of genomics research across Texas A&M has necessitated adding an active technology development program. This process taps into and supports the rich research programs at Texas A&M for information and ideas. Additionally, new bioinformatics software and methods are constantly being added as our staff are challenged with novel projects. For bioinformatics support, the core currently has seven dedicated bioinformatics scientists.

  • Custom Scripting & Specialty Projects
    • We frequently provide bioinformatics solutions tailored to the needs of idiosyncratic and specialized projects
  • Statistical Analysis and Interpretation
    • We provide novel statistical modeling and analysis capabilities for analytics based research projects
  • Base Calling
    • We correct for cross-talk, (pre)phasing, AND signal decay, accumulation, and mixed signal bias
  • Read Filtering & Cleaning
    • We actively minimize unnecessary read loss, demultiplex pooled samples, and trim technical artifacts
  • Exhaustive Quality Control
    • We use an extensive panel of QC measures to evaluate our outcomes against industry performance
  • De Novo Assembly
    • When alignments are not possible, we have the computational resources to produce top grade contigs. Review

Great information site describing bioinformatics software.

So you want to be a computational biologist?  Great advice for those who want to work in computational biology.

TEES/AgriLife Center for Bioinformatics and Genomic System Engineering 

Computing:

 Texas A&M High Performance Research Computing (22,656 total cores) and Brazos Cluster (2,400 cores) as needed.