Bioinformatics & DNA Tools

Bioinformatics

Modern molecular biology is impossible without access to the tools needed for everything from basic sequence management software and primer calculators to informatics databases and reference managers.

This page will serve as an ever-growing repository of some of the most necessary DNA tools that the OUGF is aware of, and it will continue to grow as new and better resources become available.

Computing Power

The High Performance Computing (HPC) Cluster at Ohio University:

• Four Dell PowerEdge R7515 type servers each with 64 physical AMD CPU cores and 1TB of RAM for a total of 256 CPU cores, 512 GHz of capacity, 4 TB of RAM, and 50 TB of local storage.
• The servers are integrated using VMware's vSphere as the hypervisor and vSAN as the clustered disk file system. Ubuntu Linux servers are dynamically provisioned on demand with 8 vCPU and 16 GB of RAM per system using VMware's Horizon View desktop virtualization software. Larger systems can be provisioned as needed upon request.
• The Ubuntu Linux servers can be accessed by authorized faculty and students via Ohio University's network either through Horizon View's virtual desktop (VDI) or Ohio University's campus Virtual Private Network (VPN) software.
• For access to the server please fill out this form.

Publication and Sequence Databases

The National Center for Biotechnology Information is run by the National Library of Medicine and the National Institutes of Health. This database includes sequence information (Genome, Gene, SNP, etc.), experimental data (GEO, BioSystems, ClinVar, etc.), software (BLAST, COBALT, OSIRIS, etc.), literature (PubMed, MeSH database, Bookshelf, etc.), and much more. A good place to start is the NCBI handbook and their training and tutorials.

The European Bioinformatics Institute is the European counterpart to NCBI

The Joint Genome Institute is run by the Department of Energy and has a huge suite of Data and Tools for finding sequences, genomes, proteomes, and many cross-referenced databases for assembly of large sets of information.

The Ohio University Library has access to a large number of peer reviewed journals and several large publication databases.

Sequence Management and Manipulation Software

CLC Genomics Workbench

• CLC Genomics Workbench is licensed software for sequence storage and manipulation (cloning, primer design, restriction mapping, etc.) as well as NGS data analysis. The OUGF currently maintains two licenses for this software. For information on how to access CLC Genomics Workbench please email Dr. Nigel Daniels
• The CLC Tutorials and Manual are both good resources for getting started.

CLC Sequence Viewer

• The slimmed down version of CLC. Capable of basic sequence manipulation and viewing. Most analysis and files created in Workbench are viewable in Sequence Viewer.
• A huge directory of bioinformatics tools, databases, and other resources.

QIIME 2.0

• QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. The current standard for microbiome analysis.
• QIIME 2.0 has many tutorials to follow and can be learned even if you are not familiar with Linux/Command Line Tools. Microbiome Analysis with QIIME2:A Hands-On Tutorial, another good tutorial.

Others

IDT Oligo Analyzer

• Primer design tool for calculating the melt temp, GC content, dimerization, and other characterization of primers
• IDT also maintains tools for Primer design for qPCR experiments

Galaxy

• Workflow design for automating analysis of large datasets and batches

Quick Calculators

• A set of calculators for quick use in statistics, data simulation, molarity calculators, and many more.