Bioinformatics Services

Who We Are

The mission of the Bioinformatics team at HPCC is to:

Enable the research of OSU faculty in broad areas of science where bioinformatics is useful
Empower researchers from the undergraduate to faculty level by facilitating the growth and development of computational skills pertaining to bioinformatics research.

We provide research and training support to OSU researchers located across different colleges and in all disciplines where bioinformatics analysis can facilitate new discoveries through fundamental and applied research.

Our team currently consists of bioinformaticians Dr. Chelsea Murphy and Dr. Fares Najar, HPCC Director Dr. Pratul Agarwal, and assistance from Dr. Benny Borin. The Bioinformatics team also works in close coordination with other HPCC staff who oversee and supervise the computational framework, including the supercomputer Pete and TIGER.

Our Team

Dr. Fares Z. Najar

Expertise and Background: Bioinformatics, Metabolism, OMICS, Education

Links: Google Scholar | ORCID | Bibliography

Dr. Chelsea L Murphy

Expertise and Background: Bioinformatics, Microbiology, Meta-omics, Machine learning

Links: Google Scholar | ORCID | Bibliography

Dr. Veniamin (Benny) Borin

Expertise and Background: Biochemistry, Biophysics, Protein Structure, Enzymes, High-performance computing

Links: Google Scholar

Dr. Pratul Agarwal

Expertise and Background: Biochemistry, Biophysics, Protein Structure, Enzymes, High-Performance Computing

Links: Google Scholar | ORCID

Services

Research Support

Our combined expertise in bioinformatics includes numerous programs and softwares. Some of these projects and tools include:

- Genomic sequence analysis (for conserved residues and mutations identification)
- 16S community studies
- Metagenomic assembly
- RNA-seq
- DNA methylation
- Phylogenetic tree construction
- Protein structure analysis
- Computational modelling (molecular dynamics simulations)
- BLAST
- R
- Python

We also offer experimental design, consultation, and grant/manuscript writing services. Our bioinformatics skills are the results of our lab experiences in life sciences; namely microbiology and biochemistry. To that end, we also help in experimental design before any data is generated, to ensure that you will collect the data required to answer your research question. Moreover, we can help interpret, formulate hypotheses, and design subsequent sets of experiments if needed.

Education & Training

We provide education and training opportunities at several different levels.

- Workshops & Seminars are offered regularly throughout the year, focusing on different topics ranging from an introduction to supercomputing and the command line to advanced topics on specific analyses such as RNA-seq. Check the schedule HERE.
- Group training is offered by request, and can be tailored to your lab's interests. Past trainings have included topics such as mining homologous genes from databases to phylogenetic tree construction and visualization.
- Individual training is the most frequent form of outreach that is provided when you contact us. We work with you to help you develop the skills needed for your specific project, offering troubleshooting and advice specific to your dataset.

Internship Opportunities

We can provide internship opportunities on a case-by-case basis for highly interested students, pending scheduling availability. For more information, contact director-hpcc@okstate.edu.

Costs

The primary funding model for larger projects is cost-recovery. Smaller projects are provided support at no cost. Funding is not required to initiate a discussion and request research support or training. Contact us and we will discuss with you what support is available at no cost for your research and training needs.

Acknowledging the team

In general, any time HPCC resources (computational or staff) are used in the production of a paper, the HPCC and/or the specific staff members must be given acknowledgements. Should the resources provided result in a significant amount of text and/or contribution, we ask to be included in the author list.

For more details on acknowledging the HPCC, see here.

Publications

Publications produced in coordination with the Bioinformatics team:

Wiki

The HPCC Bioinformatics team is working to build a wiki resource of submission scripts and pipelines for researchers. To learn more or gain access, contact director-hpcc@okstate.edu.