Bioinformatics

We provide bioinformatics research support and teaching both in Wooster (Jelmer Poelstra) and Columbus (Stephen Opiyo).

Bioinformatics research support

Our typical bioinformatics support model involves working closely together with researchers to help them analyze their omics data, including with 1-on-1 teaching sessions and regular progress meetings. This way, we hope to enable researchers to become proficient in these analyses themselves.

Alternatively, we can process and analyze omics data for you, using standardized or custom pipelines. For example, we can run pipelines to generate count tables from raw FASTQ files for microbial metabarcoding or RNAseq projects and we can assemble and annotate genomes.

If you are planning to generate high-throughput sequencing data and know that you will need help with its analysis, it is best to contact us well in advance, so we can create a plan for the analysis and get you up to speed with some of the computing fundamentals.

The most common types of projects that we work with are:

  • RNAseq
    • Including dual-RNAseq, where samples contain both host and pathogen RNA
    • Most projects are reference-based, but we also perform transcriptome assembly and annotation
  • 16S/ITS microbial metabarcoding
  • Eukaryotic genome assembly and annotation
  • Large-scale bacterial isolate whole-genome sequencing (including, e.g., the identification of AMR genes)
  • Comparative genomics and phylogenetics

Additionally, we have in recent years provided support for projects involving shotgun metagenomics, small RNAseq, and various custom bioinformatics analyses, and have expertise in reduced representation sequencing (RADseq/GBS) and population genetics.

Currently, all computing happens at the Ohio Supercomputer Center (OSC), where we have a large project that our members can access for data storage and computing. We exclusively use freely available software and no longer have any software licenses.

Don't hesitate to contact us for a consultation or to explore your options.

Upcoming and ongoing teaching

We regularly teach workshops, working groups, guest lectures, and graduate-level courses, sometimes in collaboration with faculty.

Given our small size, we do not have a schedule of re-occurring workshops but are always open to suggestions to organize something about a given topic — feel free to get in touch. Faculty, please contact us if you are interested in having us guest lecture in your course, or in co-teaching a workshop or so with a bioinformatics component. Besides the data and analysis types mentioned above (RNAseq, metabarcoding, etc), topics can include:

  • Genomics and applied bioinformatics in general 
  • Using the Unix shell
  • Using command-line bioinformatics tools, including writing shell scripts
  • Working at the Ohio Supercomputer Center (including with Slurm to submit jobs and Conda or Singularity to manage software)
  • Coding in R or Python
  • Formal workflow management (Nextflow or Snakemake)
  • Reproducibility and version control
 
SPRING 2024 COURSES
  • Practical Computing Skills for Omics Data (PLNTPTH5006)
    3 credit hours, Tue/Thu 2:20-3:40 pm, taught by Jelmer Poelstra
  • Introduction to statistics using R/RStudio (PLNTPTH8300)
    2 credit hours, Tue 11:30 am - 1:20 pm (7 weeks), taught by Stephen Opiyo
Practical Computing Skills for Omics Data
 
OSU CODE CLUB

Since November 2020, we have been running OSU Code Club, a weekly meeting to teach –mostly R– coding in an informal setting.

Code Club has been organized in collaboration with Jessica Cooperstone (HCS / FST), Michael Broe (EEOB; through spring '23), Mike Sovic (CAPS; through spring '23), and Horacio Lopez-Nicora (PlantPath; from fall '23).

The Code Club websites contain all teaching materials for previous Code Club sessions:

Code Club

Online teaching materials

The list below contains links to all teaching materials for a selection of previous workshops, working groups, and courses:

Membership information

  • We request that anyone receiving structural bioinformatics support obtain an MCIC Bioinformatics Membership, and whenever appropriate, offer co-authorship to the bioinformatician you receive support from.
  • The monthly membership fee is $100 per person and needs to be purchased for a minimum of six months (contact us for special rates for multiple members from the same laboratory). To become a member, please complete the online registration form.