Software Catalog

Qiagen ©

CLC Bio: Genomics Workbench

CLC Genomics Workbench is a user-friendly bioinformatics software solutions allow for comprehensive analysis of your NGS data with seamless connection with Qiagen IPA, IVA, QCII translational, OmicSoft, TRANSFAC suite of tools locally or cloud enabled solutions. It provides de novo assembly of whole genomes and transcriptomes, resequencing analysis (WGS, WES and targeted panel support), variant calling, bulk RNA-seq, ChIP-seq, DNA methylation (bisulfite sequencing analysis), and single cell RNA-seq.

Analyze your RNA-seq and small RNA (miRNA, lncRNA) data with easy-to-use transcriptomics workflows for differential expression analysis at gene and transcript levels.

Uncover critical correlations between microbiota, its metagenome and host. Making sense of complex metagenomic data becomes easy through tools and streamlined analysis workflows for gene finding, annotation, taxonomic and functional microbiome analysis. Also, make use of the full epidemiological tool set and Antimicrobial Resistance database. Supported NGS platforms are Illumina, IonTorrent, PacBio, GeneReader, Oxford Nanopore, and 10X Genomics. Read more about latest improvements.

Vendor: https://www.qiagenbioinformatics.com/products/clc-genomics-workbench 

TBI site: CLC Bio

-  User Guide

- Training Materials

CLC Bio: Main Workbench

Sanger data and expression (microarray) analysis

CLC Main Workbench is used for DNA, RNA, and protein sequence data analysis. The workbench provides variety of functionality include sanger sequence/expresion analysis, primer design, molecular cloning, phylogenetic analysis in an intuitive graphical user-interface, and sequence data management to support efficient collaboration within research groups to share data and analysis results.  CLC Main workbench is available on Windows, Mac OSX, and Linux platforms.

Vendor: https://www.qiagenbioinformatics.com/products/clc-main-workbench/

             Main Workbench features

TBI site: CLC Bio

-  User Guide

-  Training Materials

IPA:  Ingenuity Pathway Analysis

Ingenuity® Pathway Analysis (IPA®) is a powerful analysis and search tool that uncovers the significance of ‘omics data and identifies new targets or candidate biomarkers within the context of biological systems. IPA has been adopted by the life science research community and is cited in thousands of articles for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNA-seq, small RNA-seq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments.

Vendor: https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/

TBI site: IPA

-  User Guide

-  Training Materials

OmicSoft - Array Studio

OmicSoft is a market-leading provider of biomarker data management, visualization, and analysis products. OmicSoft’s products are based on “Lands,” which are curated and standardized public data sets in oncology (“OncoLand”), major disease areas, including immunology and cardiovascular disease (DiseaseLand) and genetic research (GeneticsLand).

The product portfolio also includes “Array Server,” OmicSoft’s enterprise-scale, multi-omic data management offering, and “Array Studio,” a graphical user interface to browse, analyze and visualize data from NGS sequencing, microarray and other technologies.

OmicSoft enables novel discoveries using Qiagen Ingenuity Pathway Analysis IPA and Omicsoft Array Studio software by integrating user data with public data from repositories such as GEO, Array Express, TCGA and others. The integrated data can be used to develop hypothesis-driven discoveries associated with biomarkers, drug targets, key regulators, pathways, and novel biological mechanisms that support a managed, collaborative, project-based, cloud-enabled user-friendly environment to accelerate translation research.

Vendor: http://www.omicsoft.com/

TBI site: OmicSoft

-  COH User Guide

-  Training Materials

QCII-T: QCI Interpret Translational

QCI Interpret Translational is a NGS variant assessment software that enables rapid, evidence-powered variant annotation, filtering, and triaging for human exome, genome, and large cohort sequencing data.  QCI Interpret Translational improves research efficiency and accuracy by automating manual curation processes, dynamically and transparently assessing variants according to society guidelines with full user-control, and optimizing resource allocation, allowing users to focus on what matters most: transforming genomic data into publishable insights.

Vendor: Qiagen QCII-Translational

TBI site: QCII-T

-  User Guide

-  Training Materials

MacVector ™

MacVector

MacVector

MacVector is a comprehensive Macintosh sequence analysis application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.

Other major MacVector features

Assembler

Assembler is an add-on DNA sequence assembly module for MacVector that provides a simple graphical interface to the phred, phrap and cross_match contig assembly algorithms from the University of Washington, the popular Bowtie fast reference alignment program for Next Generation Sequencing projects and the Velvet, SPAdes and Flye de novo assemblers for NGS data. Assembler must be purchased separately from MacVector. 

Vendor: https://macvector.com/

TBI site:  MacVector

-  User Guide

-  Training Materials

Wolfram ©

Mathematica

Mathematica is primarily aimed at technical computing for R&D and education. Based on the Wolfram Language, Mathematica is 100% compatible with other core Wolfram products.

Full Wolfram Language Documentation & Reference  

Vendor: Wolfram

TBI site: Mathematica

-  User Guide

Mathworks ©

MATLAB

MATLAB® combines a desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly.

Toolboxes are professionally developed, rigorously tested, and fully documented.

Apps let you see how different algorithms work with your data. Iterate until you’ve got the results you want, then automatically generate a MATLAB program to reproduce or automate your work.

Scale your analyses to run on clusters, GPUs, and clouds with only minor code changes. There’s no need to rewrite your code or learn big data programming and out-of-memory techniques.

Vendor: www.mathworks.com

TBI site: MATLAB

-  User Guide

-  Training Materials

Thermo Fisher

Oncomine

The Oncomine database was taken offline and discontinued by the vendor effective January 17, 2022. There is no replacement for this service.  If you have questions, please contact Yate-Ching Yuan, PhD.

Oncomine is a private subscription service.

Oncomine™ Platform Software provides solutions for individual researchers as well as collaborative consortia, with robust, peer-reviewed analysis methods and a powerful set of analysis functions that compute gene expression signatures, clusters, and gene-set modules, automatically extracting biological insights from the data.

Vendor: Thermo Fisher

TBI site: Oncomine

Vendor support: Thermo Fisher

Partek ©

Partek Flow

Partek Flow® is a Web based start-to-finish software analysis solution for next generation sequencing data applications. Partek software enables researchers to easily perform genomic data analysis without ever needing to write a single line of code or sacrificing statistical power or advanced functionality. From alignment to pathway analysis, Partek provides a seamless, integrated analysis solution on a single platform that provides the power of a cloud or cluster when needed, and the convenience of desktop software for less compute intensive tasks. Enter the analysis pipeline where it makes sense for your study.

• Supports NGS and microarray applications such as single cell gene expression, bulk RNAseq, miRNAseq, non-coding RNAseq, DNAseq, ChIP-seq, microarray, metagenomic, microbiome, and methylation
• All the tools you need to quickly go from raw data files to meaningful results within a single solution
• Enter the pipeline where it makes sense for you; raw data, aligned reads, count data, or normalized counts
• Explore data with interactive, customizable, and publication-ready visualizations

Vendor: https://www.partek.com/partek-flow/

TBI site: Partek

-  User Guide

-  Webinars

-  Training Materials

Partek ©

Partek Genomics Suite

Partek^® Genomics Suite^® is a statistical analysis software that lets you analyze microarray, qPCR, and pre-processed NGS data right from your desktop computer. It is fast, agile, and memory efficient. With a user-friendly interface, rich visualizations, and guided workflows for common genomics assays, Partek Genomics Suite gives biologists, bioinformaticists, and statisticians a single, integrated solution for trustworthy results.

Vendor: https://www.partek.com/ partek-genomics-suite /

TBI site: Partek

-  User Guides

-  Training Materials

Schrödinger

Schrödinger Suite

The Schrödinger platform integrates predictive physics-based methods integrates differentiated solutions for predictive modeling, data analytics with machine learning techniques and enabling collaboration for computer assisted molecular design and drug discovery. Its iterative process is designed to simulate molecular interactions among protein, DNA/RNA, and millions of chemical in silico ahead of synthesis and assay to accelerate validation and optimization in web lab. The platform powers the drug discovery efforts, from target identification to hit discovery to lead optimization. It also drives our research collaborations and enables discovery of high-quality, novel molecules more rapidly, at lower cost, and accelerate the transition from the discovery phase to the clinical trial phase for critical public health needs. 

• Use PyMOL to view, share, and analyze molecular data. In addition to being lightweight and fast, PyMOL can create images of peerless visualization quality, while offering the flexibility of Python-based development and scalability.
  https://www.schrodinger.com/products/pymol

• Maestro is the portal to all of Schrödinger's computational technology – far more than just a user interface, Maestro also helps researchers organize and analyze data.
  https://www.schrodinger.com/products/maestro

Vendor:     https://www.schrodinger.com

                  https://www.schrodinger.com/drug-discovery

TBI site: Schrödinger

-  User Guides

-  Training Materials

COH-developed

BD-Func

BD-Func is a streamlined algorithm for predicting activation and inhibition of pathways.

Citation: Warden CD, Kanaya N, Chen S, Yuan YC. BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. PeerJ.  2013 1: e159. PubMed PMID: 24058887; PubMed Central PMCID: PMC3775632. PubMed:  Article link

TBI site: BD-Func

Source code and download:

Sourceforge-BD-Func

COH-developed

COHCAP

COHCAP is an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.

Citation: Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC.  COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res, 2019, Sep 5;47(15):8335-8336 PubMed PMID: 23598999.  PubMed:  Article link

TBI site: COHCAP

Source code

COHCAP - Bioconductor

DNAnexus ®

POSEIDON

Precision Oncology Software Environment Interoperable Data Ontologies Network is a secure, cloud-based Oncology Insights Engine enabling exploration, analysis, visualization, and collaboration on our patient clinicogenomic data.  This platform gives investigators a tool that can be utilized from cohort discovery, preliminary feasibility testing all the way through to drawing patient specific insights.

Vendor: https://www.dnanexus.com/

Center for Informatics
Allen Mao | Sr Manager, Research Informatics

C4i site: POSEIDON

Clarivate Analytics

EndNote

-  EndNote is a commercial reference management software package, used to manage bibliographies and references when writing essays and articles.

-  Bibliographic management software for managing bibliographies and formatting research publications. This tool would be used by anyone who needs to manage bibliographic references for their research, professional development, and publishing.

Vendor:     https://endnote.com/product-details/

Graff Library
Keir Reavie | Director, Library Services

Clarivate Analytics

Metacore

Clarivate’s bioinformatics solution, MetaCore website, is used for multi-omics analysis, studying various pathways, biomarkers, and allows the ability to upload your own data for analysis. Researchers use Clarivate data analysis tools of manually curated biological pathways and interaction information to:

• Identify novel drug targets, mechanisms, and biomarkers through multi-omics analysis
• Compare and contrast ‘omics’ datasets and conduct enrichment analysis across multiple functional ontologies
• Knowledge mine for prior research and datasets related to diseases, human processes, genes, proteins, and targets of interest.

Sponsor: https://ostr.ccr.cancer.gov/bioinformatics/software/clarivate/

Graff Library
Keir Reavie | Director, Library Services

SharePoint site: MetaCore

- Training Materials

American Chemical Society® 

SciFinder

SciFinder is a platform from Chemical Abstracts Service that provides the most comprehensive and accurate collection of chemical reactions, substances, and scientific literature curated by scientists. SciFinder provides tools to search for chemical substance information, chemical structures and reactions, and references to the latest scientific literature from approximately 50K journals. The service also provides access to approximately 18 million searchable, full-text patents from 46 major patent offices across the globe. SciFinder is an important resource for supporting pharmaceutical research and development.

Vendor: https://www.cas.org/solutions/cas-scifinder-discovery-platform/cas-scifinder

Graff Library
Keir Reavie | Director, Library Services

SharePoint site: SciFinder

- Training Materials

BioRender

BioRender

BioRender is a web-based, easy-to-use science illustration tool.  It lets users create high-quality professional diagrams for publications, presentations, posters, patents, outreach and more - 50x faster than current alternatives with no drawing skills required.

The BioRender Learning Hub offers free, on-demand tutorials: https://learn.biorender.com/

Vendor: BioRender

Hosted by ITS Research IT

Contact Krish Rajagopal for access and user support.

PerkinElmer Informatics

ChemDraw

ChemDraw a drawing tool that allows users to draw chemical structures and reactions as well as biological objects and pathways. Users can also use it to predict properties and spectra, convert chemical structures to IUPAC names, view 3D structures, etc.

Vendor: PerkinElmer Informatics

Hosted by ITS

Contact “Rudy” Rodolfo Mortero for access and user support.

GraphPad Software, Inc.

Graphpad Prism

- GraphPad Prism, available for both Windows and Mac computers, combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization.

- GraphPad Prism is designed for experimental biologists in medical schools and drug companies, especially those in pharmacology and physiology. It is also used broadly by biologists, social and physical scientists, undergraduate and graduate students.

Vendor: www.graphpad.com

Hosted by ITS

Contact “Rudy” Rodolfo Mortero for access and user support.

GSL Biotech LLC

SnapGene

SnapGene is a molecular biology software used to easily plan and simulate your DNA manipulations, visualize ORFs, reading frames, and primer binding sites, automatically record the steps in a cloning project, and share annotated sequence files with other researchers.

Vendor: www.snapgene.com 

Hosted by ITS Research IT

Contact Krish Rajagopal for access and user support.

geneXplain ©

TRANSFAC

-  TRANSFAC® is the database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Dating back to a very early compilation, it has been carefully maintained and curated since then and became the gold standard in the field, which can be made use of when applying the geneXplain platform.

-  Knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes.

Vendor: http://genexplain.com/

Hosted by IGC/Integrated Genomics Core

Contact Xiwei Wu, PhD for  access and user support.