GALILEO@UGA Subject Guides: Bioinformatics: Software & Tools

Main Library & McBay Science Library

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Main Library	7:30am – 2:00am
Circulation Desk	7:30am – 2:00am
Digital Humanities Lab	7:30am – 2:00am
Interlibrary Loan Office	8:00am – 5:00pm
Reference Desk	9:00am – 10:00pm

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Data Services at UGA

Did you know that UGA Libraries has a DigiLab that offers workshops, tutorials, and consultations to help you with your research needs. They also host office hours on Wednesday from 1:30pm - 3:00pm in the Main Library and McBay Science Library. Click here to see what software is available throughout all library locations.

All UGA students, faculty and staff have free access to LinkedInLearning with their MyID. Available courses include Python, R, SAS, and SPSS.

Online Analytical Tools

A number of online analytical resources exist where researchers can take advantage of high performance computing clusters to analyze large-scale datasets. The resources listed here are just a few of the most commonly used tools in the field of bioinformatics.

CyVerse
CyVerse provides a national cyberinfrastructure for life science research as well as training scientists in using such high performance computing resources. Formerly the iPlant Collaborative, CyVerse provides a platform for data storage, bioinformatics tools, image analyses, and cloud services. CyVerse also allows programmatic access through multiple APIs. The CyVerse Learning Center provides valuable information for getting started using CyVerse resources.
Galaxy
Galaxy is a platform for performing data-intensive biomedical research. This open source project can be used either on the free, public server or as your own instance. With thousands of tools available, Galaxy allows you to build robust, reproducible bioinformatic pipelines. You can also use one of the hundreds of published workflows for analyzing your own data. A number of Galaxy tutorials are available, providing examples of how to use Galaxy.
GEO2R
GEO2R can be used to perform differential gene expression analyses on datasets that are hosted at NCBI's Gene Expression Omnibus. The tool allows you to define how samples are compared and offers flexibility in significance calculations and output formats. Best of all, all the calculations are performed in real-time with a dynamically generated R script which can be copied and used on your own data!
E-utilities
The E-utilities API provides programmatic access to several NCBI databases, including PubMed, Genome, Nucleotide, and dbSNP; this API allows you to perform queries without using a web browser. EDirect is a library of perl scripts that offers UNIX command-line utilities for automating E-Utilities queries and processing results.
Gene Ontology Consortium
The Gene Ontology Consortium has produced a suite of tools available through the AmiGO site. In addition to navigating Gene Ontology annotations, AmiGO offers enrichment analysis tools and an SQL interface for querying the GO database.
CIPRES
Providing cyberinfrastructure for evolution research, CIPRES is a public resource for the estimation of large phylogenetic trees. The high performance inference tools include RAxML and MrBayes. A number of sequence alignment tools, including MAFFT, MUSCLE, and ClustalW are also available. Online tutorials show how to use the data management and analytical resources available at CIPRES.

Learn to Code

A key skill in bioinformatics is the ability to interpret and write computer code for custom analyses. There are many resources for leaning how to write computer code, including online instruction, Software and Data Carpentry workshops, UGA DigiLab workshops, and LinkedIn courses. If you are just starting out, and want to learn how to write computer code for bioinformatic analyses, here are a few places to start:

R language:

To get started in R, check out Swirl, which provides an interactive interface to the R language.
Software Carpentry has two introductory lessons for learning R (Lesson 1, Lesson 2), both designed for novice audiences.

Python:

Learnpython.org is an online interactive resource for learning python.
Software Carpentry has an entry-level python workshop.
Finally, the classic Learn Python the Hard Way, has been used by millions to learn basic through advanced topics of this powerful scripting language.

Linux:

Familiarity with the command-line interface of the Linux shell is a very important skill in bioinformatics, and you can get started with a novice lesson from the Software Carpentry Foundation.
There is also an interactive learning resource at learnshell.org.
And be sure to check out this YouTube video from NCBI on basic Linux commands.