Bioinformatics

IHRC offers a robust suite of bioinformatics consulting, analytical services, and bioinformatics workforce development training through IHRC resources and IHRC’s Applied Bioinformatics Laboratory (ABiL).

Our highly qualified bioinformaticians, our network of subject matter experts, and our partnership with the Bioinformatics program of the Georgia Institute of Technology allow us to remain at the cutting edge of bioinformatics and incorporate the latest innovations into the solutions that we provide. We work closely with our clients to assess their project requirements and we design, develop, and implement cutting edge bioinformatics solutions and data management systems to address their objectives in research, precision medicine and other areas. Our extensive experience providing bioinformatics solutions includes molecular epidemiology services, and support for transmission, vaccine effectiveness, carriage and other studies, as well as outbreak response support.

We have been providing Bioinformatics support to the Centers for Disease Control and prevention since 2011 and Bioinformatics Workforce Development Training to CDC since 2014.

Bioinformatics Services

Genomics, Transcriptomics & Proteomics
Typing
Custom Scripting & Algorithm Development
Data Management, Cloud & High Performance Computing

Whole Genome de novo Assembly and Annotation
Genome Mapping / Resequencing
SNP/ Indel / SV/ Discovery and Annotation
Genome finishing / gap closure analysis
Functional Genomics
Genome Wide Association Studies
Comparative Genomics
Detection of Virulence Factors

Genotype-Phenotype Relationship
Metagenomics
Transcriptomics
Whole Transcriptome de novo Assembly and Annotation
Expression Analysis
Copy Number Variation (CNV) Analysis
Proteomics
Protein modeling

Molecular Epidemiology
Phylogenetics
Multi Locus Sequence Typing
Genomic Typing
Development of Novel Typing Schemes

Machine Learning
Custom Scripting
Custom Algorithm Development
Custom Pipeline Development
Development of Cutting Edge Bioinformatics Tools
Statistical Analysis

Creation of Custom Databases and Web Interfaces
Big Data
High Performance Computing
Cloud Computing

The IHRC Applied Bioinformatics Laboratory (ABiL)

IHRC offers bioinformatics consulting and data analysis on a per-project basis as well as bioinformatics workforce development training through the IHRC Applied Bioinformatics Laboratory (ABiL). Projects submitted to ABiL are examined by a team of highly qualified bioinformaticians to deliver the most comprehensive analysis.

Bioinformatics Workforce Development Training

ABiL’s Workforce development training courses are designed to train professionals in the use of the latest bioinformatics tools. The ABiL curriculum is based upon the active-learning paradigm, and is applied in a modular fashion, in the form of short or long courses focused on a particular area of bioinformatics. Participants receive hands on training working with real bioinformatics data in a bioinformatics computational environment. Courses can be delivered at the ABiL training site on the campus of the Georgia Institute of Technology, or at the client site nationally or internationally. Basic, intermediate and advanced levels of training are available in the form of semester based courses (9 weeks), modules (4 days), and sub modules (2 days), all of which can be fully customized to a client’s needs . Descriptions for all ABiL workforce development training courses appear below, and the full course description booklet in PDF format can be downloaded by clicking on the appropriate link.

Modules PDF

Sub-Modules PDF

Semester Courses PDF

Workforce Development Modules
Workforce Development Sub-Modules
Workforce Development Semester Courses

Introduction to Scientific Computing

This intermediate level bioinformatics module provides participants with the essential skills required to be able to work in a Linux/*nix system when performing bioinformatics analyses. The participants will receive instruction in basic command line Linux and system administration, and will be instructed in the compilation and installation of software in the Linux environment. Topics covered include the basics of Linux and file systems, file access, file handling, searching and regular expressions, pipeline development and shell scripting. At the conclusion of the course, participants should have sufficient knowledge to develop their own working pipelines and shell scripts that can be applied to their research. The whole course will be geared towards application of Linux in bioinformatics.

Introduction to Computational Microbial Genomics

This intermediate level bioinformatics module provides participants with the opportunity to gain hands on experience working with numerous bioinformatics programs and protocols that are commonly used for the computational analysis of microbial genome sequences. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis of next-generation sequencing (NGS) data. Course material includes discussions and exercises involving NGS read quality assessment, genome assembly, gene/feature prediction, functional annotation, multi-locus sequence typing, average nucleotide identity, virulence factor detection, horizontal gene transfer detection, genome alignment and visualization and microbial genomics databases. Visualization techniques to assist in the analysis and presentation of results will also be demonstrated. Bioinformatics programs for which instruction is provided include webservers, graphical user interface (GUI) and command line tools such as FastQC, Velvet, Prodigal, RNAmmer, BLAST, SignalP, Pfam, InterPro, MEGA, JSpecies, TM4 MeV, Alien_hunter and Mauve. Discussions and tours of microbial genomics databases include NCBI and KEGG.

Computational Sequence Analysis

This intermediate level bioinformatics module provides participants with the opportunity to gain hands on experience working with numerous commonly used bioinformatics programs and includes descriptions of the theories and protocols used to perform various types of analyses of molecular sequences. The participants will receive instruction in basic command line Linux and gain experience working at the command line throughout the module. Participants will be instructed in the methods and tools for aligning short read sequences to a genome, calling variants, aligning a pair of or multiple short sequences, the basics of molecular phylogenetics, utilizing sequence alignment for database searching, aligning a pair of or multiple genomes, predicting features in a genome and protein and structure representation. Bioinformatics programs for which instruction is provided include graphical user interface (GUI), webservers and command line tools such as FastQC, BWA, SAMtools, BCFtools, the EMBOSS suite, MEGA, Mauve, Prodigal, Glimmer, RNAmmer, Jmol, JSpecies and BLAST among others.

Introduction to Bioinformatics Databases

This intermediate level bioinformatics module provides participants with an overview of different database resources available for bioinformatics along with some discussions on implementation of bioinformatics databases and their associated tools. Course material includes an introduction to bioinformatics, next-generation sequencing (NGS) technologies, database searching utilities, access and retrieval of data from various general and specialized databases and the basics of setting up custom built databases. Databases that will be discussed include NCBI, specialized databases for functional annotation, human health related databases, Kyoto Encyclopedia of Genes and Genomes (KEGG), Virulence Factor Database (VFDB), metagenomics databases and PubMLST. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analyses.

Comparative Genomics

This intermediate level bioinformatics module provides participants with the commonly used methods and techniques used for comparative analysis of genomic features. Course material includes discussions and exercises on the techniques for aligning molecular sequences, methods for performing genome-scale comparisons and some of the molecular typing tools. The participants will be instructed on aligning a pair of or multiple short sequences, molecular phylogenetics, sequence based database searching, aligning a pair of or multiple genomes, multi-locus sequence typing and gene/protein clustering. Discussions and exercises are included with each of the topics as well as time where the participants can practice the techniques on their own. Tools that are used include graphical user interface (GUI), webservers and command line tools such as the EMBOSS suite, MEGA, BLAST suite, JSpecies and Mauve among others. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis.

Genomics Approaches to Molecular Epidemiology and Typing

This intermediate level bioinformatics module provides participants with methods for the identification and in silico typing of pathogens in outbreak control. Course material includes the evolutionary underpinning of MLST based typing methods, the concept of MLST, its current implementation, associated resources and tools, next-generation sequencing (NGS) technologies and their influences on MLST, variant detection and the concept of SNP based typing and the general concepts behind creation of custom typing schemes. Participants will also be instructed on underlying algorithms for the tools covered. Tools that are used include a mix of graphical user interface (GUI), webservers and command line tools such as MEGA, PubMLST, Velvet, SOAPdenovo2, QUAST, CISA, BLAST, JSpecies, BWA, SAMtools, BCFtools and IGV among others. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis.

Clinical Metagenomics

This intermediate level bioinformatics module provides participants with concepts and methods involved in clinical metagenomics. Course material includes the next-generation sequencing (NGS) technologies, contemporary computational genomics techniques, metagenomics and analytical protocols in clinical projects. Participants will also be instructed on underlying algorithms for the tools covered. Tools that are used include a mix of graphical user interface (GUI), webservers and command line tools such as FastQC, Velvet, SOAPdenovo2, BLAST, JSpecies, BWA, SAMtools, BCFtools, IGV and Kraken among others. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analyses.

The National Center for Biotechnology Information

This intermediate level bioinformatics module provides participants with the opportunity to gain hands on experience working with different components of NCBI used for bioinformatics analysis. Course material includes discussions and ecercises on NCBI’s sequence storage format, tour of different components of NCBI, sequence searching through BLAST and its variants, programmatic access to NCBI, writing custom data analysis pipelines and NCBI’s Genome Workbench. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis.

Perl for Bioinformatics Programming

This intermediate level bioinformatics module provides participants with the opportunity to gain hands on experience working with the Perl programming language, a commonly used tool in the analysis of biological data. Course material includes the basics of programming concepts and Perl, file access, handling and manipulation, searching and regular expressions and CPAN. By the end of the course, participants will have sufficient knowledge to develop their own working Perl scripts and pipelines that can be applied to their work and research. The whole course will be geared towards application of Perl in bioinformatics.

Next Generation Sequencing

This advanced level bioinformatics module provides participants with the opportunity to gain hands on experience in handling and analysis of next-generation sequencing (NGS) data. Course material includes bioinformatics aspects of sequencing basics, 454 sequencing, Illumina single end and paired end sequencing, genome visualization, genome mapping and variant calling. Discussions and exercises will be included with each topic and participants will be provided with adequate time to practice the techniques on their own. The module will involve a mix of graphical user interface (GUI) and command line tools such as FastQC, PRINSEQ, Ray, MIRA, Velvet, SOAPdenovo2, ABySS, QUAST, CISA, Mauve, BRIG/CCT, BWA, SAMtools, BCFtools and IGV among others. The participants will receive instruction in command line Linux and gain experience working at the command line to perform bioinformatics analysis of NGS data.

Introduction to Computational Genomics

This advanced level bioinformatics module provides participants with the opportunity to gain hands on experience in genome assembling, gene prediction and reference mapping with Next Generation Sequencing (NGS) data. Course material includes bioinformatics aspects of sequencing basics, Illumina paired-end sequencing, prokaryotic and eukaryotic gene prediction, homology based prediction validation, genome mapping and variant calling. Discussions and exercises will be included with each topic and participants will be provided with adequate time to practice the techniques on their own. The module will involve a mix of graphical user interface (GUI) and command line tools such as FastQC, PRINSEQ, Velvet, SOAPdenovo2, QUAST, CISA, GeneMark Suite, Glimmer, Prodigal, BLAST, BWA, SAMtools, BCFtools and IGV among others. The participants will receive instruction in command line Linux and gain experience working at the command line to perform bioinformatics analysis of NGS data.

High Performance and Cluster Computing

This advanced level bioinformatics module provides participants with the opportunity to gain hands on experience in learning about different computational technologies involved in providing high-performance support and cluster computing. Course material includes virtual machine and setting up your own VM instances, Linux and basic administration in Linux, utility installation, file handling, regular expression, version controls, introduction to Perl, threading and cloud computing. Discussions and exercises will be included with each topic and participants will be provided with adequate time to practice the techniques on their own. This module is geared towards helping participants gain substantial exposure to the computer technologies and will involve heavy command line usage throughout the course.

Introduction to Sequence Storage Formats

This basic level bioinformatics sub-module provides participants with the opportunity to gain hands on experience working with numerous sequence storage formats and their inter-conversions. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform the required tasks. Course material includes discussions and exercises on sequence read formats, mapping formats, variant formats, nucleotide and protein formats and alignment and tree formats. The discussions will focus on the description of the format, type of data stored, common software that can read the format and conversion of one format into other equivalent formats. Bioinformatics programs for which instruction is provided include graphical user interfaces (GUIs), webservers and command line tools such as FastQC, Mauve, IGV, Plink, BWA, SAMtools, Jmol, Cytoscape, MEGA, NCBI and EBI among others.

Sequence Alignments

This basic level bioinformatics sub-module provides participants with the opportunity to gain hands on experience working with different methods used for the alignment of DNA and protein sequences. Course material includes discussions and exercises on the understanding of tools and methods to align a pair of or multiple short sequences, utilization of sequence alignment for database searching, alignment of short read sequences to a genome and pairwise of multiple genome alignment. The scope is restricted to sequence alignments and related topics will be touched upon briefly. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform the required tasks. Bioinformatics programs for which instruction will be provided include graphical user interfaces (GUIs), webservers and command line tools such as the EMBOSS suite, MEGA, BLAST, BWA, CCT and Mauve among others.

Bioinformatics Programming Basics

This basic level bioinformatics sub-module provides participants with the essential skills required to be able to work in a Linux/*nix system when performing bioinformatics analyses. The participants will receive instruction in basic command line Linux and system administration and will be instructed in the compilation and installation of software in the Linux environment. Topics covered include the basics of Linux and file systems, file access, file handling, pipeline development and shell scripting. At the conclusion of the course, participants will have sufficient experience with Linux to begin using it in their research. The whole course will be geared towards the basic application of Linux in bioinformatics.

Introduction to Bioinformatics Databases

This basic level bioinformatics sub-module provides participants with an overview of different database resources available for bioinformatics along with some discussions on the implementation of bioinformatics databases and their associated tools. Course material includes an introduction to bioinformatics, next-generation sequencing (NGS) technologies, database searching utilities and the basics of setting up custom built databases. Databases that will be discussed include NCBI, specialized databases for functional annotation and PubMLST. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analyses.

Computational Phylogenetics

This basic level bioinformatics sub-module provides participants methods for aligning sequences and reconstructing phylogenies as a way to discover relationships between organisms through use of molecular data. Course material includes the basics of sequence alignment and the corresponding assumptions, pairwise sequence alignment, multiple sequence alignment, basics of phylogenetics and interpreting trees, methods of tree construction and their comparisons, tree view and editing and distance matrix computation. The methods covered focus on small length sequences, not long sequences such as genomes where different methods are required. Tools that are used include the EMBOSS suite, MEGA and JSpecies among others.

MLST Based Epidemiology

This intermediate level bioinformatics sub-module provides participants the concepts and methods for performing multi-locus sequence typing (MLST) for pathogen identification. Course material includes discussions and exercises on the evolutionary underpinning of MLST based typed methods, the concept of MLST, its current implementation, associated resources and tools, the basics of next-generation sequencing (NGS) technologies and their influence on MLST and variant detection for SNP based typing. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis. A mix of graphical user interface (GUIs), webservers and command line tools are included such as PubMLST, MEGA, BLAST, BWA, SAMtools, BCFtools and IGV among others.

Introduction to NCBI

This intermediate level bioinformatics sub-module provides participants with an understanding of the National Center for Biotechnology Information (NCBI), a pivotal resource in facilitating bioinformatics research by enabling data storage, retrieval and analysis. Course material covers discussions on the structure of NCBI, different component databases and their inter-connections, numerous analytical tools available in NCBI, Entrez, and the programmatic and web-based query and cess of data stored in NCBI databases. Bioinformatics programs for which instruction is provided include webservers and command line tools such as NCBI Genome Workbench, BLAST, E-Direct and E-Utils among others. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis however familiarity on Linux will be beneficial.

Protein Functional Annotation

This intermediate level bioinformatics sub-module provides participants with the methods and techniques for functionally annotating proteins and non-coding RNAs as a way to attach biological information to genomic elements. Course material includes an introduction to bioinformatics and sequence formats, annotation via homology, ab initio annotation, accessing data from NCBI, clustering analysis, using KEGG and other functional annotation databases and associated tools. Exercises consist of performing functional annotations both via webservers and the Linux command-line. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis. Bioinformatics programs for which instruction will be provided include webservers such as Pfam, InterPro and RAST and command line tools such as BLAST+ and BLAST among others.

Intermediate Bioinformatics Programming

This intermediate level bioinformatics sub-module provides participants with the opportunity to gain hands on experience working with the Perl programming language, a commonly used tool in the analysis of biological data. Course material includes the basics of programming concepts and Perl, file access, file handling and manipulation, loops, subroutines and modules. By the end of the course, participants will have sufficient knowledge to develop their own working Perl scripts and pipelines that can be applied to their research. The whole course will be geared towards application of Perl in bioinformatics.

Sequence Visualization

This intermediate level bioinformatics sub-module provides participants with the opportunity to gain hands on experience with sequence visualization. Course material includes discussions and exercises on the visualization of different types of sequences and analyses such as multiple sequence alignments, trees, read to genome mapping, genome alignments, circular genome visualization and network visualization. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analysis. Bioinformatics programs for which instruction is provided include graphical user interface (GUI) and command line tools such as MEGA, Mauve, CGView Comparison Tool (CCT), BWA, SAMtools and Cytoscape among others.

Gene Prediction

This advanced level bioinformatics sub-module provides participants with the opportunity to gain hands on experience with the techniques and methods of predicting genes and features from complete genomes and assemblies using ab initio and homology based methods. Course material includes discussions and exercises on the prediction of genes/features in both prokaryotic and eukaryotic organisms as well as in metagenomics samples, focusing on why and how the techniques for prediction differ. Also included are discussion on the algorithms and paradigms behind gene prediction and the concept of merging prediction sets to generate a more complete set. Exercises consist of performing gene (and non-coding RNA) predictions and then merging the predictions to result in a final complete set. The participants will receive instruction in Linux command line and gain experience working at the command line to perform bioinformatics analysis. Bioinformatics programs for which instruction is provided include webservers and command line tools such as GeneMark Suite, Glimmer, Prodigal, RNAmmer, AUGUSTUS and BLAST among others.

Comparative Genomics

This advanced level bioinformatics sub-module provides participants with methods of comparisons of different genomic features through sequence comparisons. Course material includes discussions and exercises on the techniques for aligning molecular sequences and methods for performing genome-scale comparisons. The participants will be instructed on aligning multiple short sequences, sequence based database searching, aligning a pair of or multiple genomes and gene/protein clustering. Bioinformatics programs for which instruction will be provided include graphical user interface (GUI), webservers and command line tools such as MEGA, BLAST suite, JSpecies and Mauve among others. The participants will receive instruction in basic command line Linux and gain experience working at the command line to perform bioinformatics analyses.

Genome Assembly I

This advanced level bioinformatics sub-module provides participants with the opportunity to gain hands on experience in handling and assembly of next-generation sequencing (NGS) data. Course material includes bioinformatics aspects of sequencing basics, Illumina paired end sequencing, and de novo genome assembly. The module will involve a mix of graphical user interface (GUI) and command line tools such as FastQC, PRINSEQ, Velvet, SOAPdenovo2, QUAST and CISA among others. The participants will receive instruction in command line Linux and gain experience working at the command line to perform bioinformatics analysis of NGS data.

Genome Assembly II

This advanced level bioinformatics sub-module provides participants with the opportunity to gain hands on experience in the handling and analysis of next-generation sequencing (NGS) data. Course material includes bioinformatics aspects of sequencing basics, genome mapping and variant calling. Bioinformatics programs for which instruction will be provided include a mix of graphical user interface (GUI) and command line tools such as FastQC, PRINSEQ, BWA, SAMtools, BCFtools and IGV among others. The participants will receive instruction in command line Linux and gain experience working at the command line to perform bioinformatics analysis of NGS data.

Computational Microbial Genomics

This bioinformatics course provides trainees experience with the commonly used bioinformatics programs and protocols for the computational analysis of microbial genome sequences. Topics covered include discussions and exercises on Next Generation Sequencing (NGS) read quality assessment, genome assembly, gene/feature prediction, functional annotation, multi-locus sequence typing, average nucleotide identity, virulence factor detection, horizontal gene transfer detection, genome alignment and visualization and microbial genomics databases. Many of these topics also include visualization techniques to assist in result analysis and presentation. The course will involve basic Linux command line usage, and sufficient information will be provided to the trainees in the first few classes of the course. Tools that are used include command line tools, GUIs and webservers such as FastQC, Velvet, QUAST, Prodigal, RNAmmer, BLAST, SignalP, Pfam, InterPro, MEGA, JSpecies, TM4 MeV, Alien_hunter and Mauve. Discussions and tours of microbial genomics databases include NCBI and KEGG.

Computational Sequence Analysis

This bioinformatics course provides trainees with the skills and knowledge necessary for various methods of analysis of molecular sequences. Topics covered include access and retrieval of sequence data, tools and methods for aligning short read sequences to a genome, calling variants, aligning a pair of or multiple short sequences, the basics of molecular phylogenetics, utilizing sequence alignment for database searching, aligning a pair of or multiple genomes and rearrangement analysis. Advanced Linux command line usage is involved and the first part of the course is dedicated to cover this. Tools that are used include GUIs, webservers and command line tools such as FastQC, BWA, SAMtools, BCFtools, EMBOSS suite, MEGA, Mauve and BLAST among others.

Linux for Bioinformatics

This bioinformatics course provides trainees with the skills to be able to productively work in a Linux/*nix system for Bioinformatics analysis. Topics covered include the basics of Linux and file systems, file access, file and data retrieval from various sources, file handling, searching and regular expressions, pipeline development and shell scripting. By the end of the course, trainees will have sufficient knowledge to develop their own working pipelines and shell scripts that can be applied to their research. The whole course will be geared towards application of Linux in Bioinformatics.

Perl for Bioinformatics

This bioinformatics course provides trainees with programming skills in Perl for Bioinformatics. Topics covered include the basics of programming concepts and Perl, file access, handling and manipulation, searching and regular expressions, CPAN, OOPs and basics of writing parallelized scripts. By the end of the course, trainees will have sufficient knowledge to develop their own working scripts and pipelines that can be applied to their work and research. The whole course will be geared towards application of Perl in Bioinformatics.