Software Available at WHSC Library

Genomic and Proteomic Analysis Tools

geneXplain | HGMD Professional | LaserGene | Metacore


geneXplain is an "online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications" and includes the following components:
  • Proteome: A powerful ontology search query system, with specialized tools for gene set analysis and pathway visualization, allows scientists working with mammalian, yeast, worm and plant species to quickly find answers to questions relevant to their research. A specialized custom sequence annotation tool allows scientists working with other species to extend predictive functions to newly sequenced or otherwise uncharacterized genomes.
  • TRANSFAC:  an internationally unique knowledgebase containing data on eukaryotic transcription factors, their experimentally-proven binding sites, and regulated genes.

Register for geneXplain

  • You must register to login to geneXplain.
  • To request a login use Ask A Librarian or email Jeremy Kupsco (jkupsco@emory.edu).
  • Logins are for use by Emory Employees only.
  • Please log off at the end of each session to prevent blocking other users access.

To log into geneXplain click here.


HGMD® Professional is a unique resource providing comprehensive data on human inherited disease mutations to genetics and genomic research. It allows you to: 

  • Prioritize mutations from whole exome or whole genome sequencing.
  • Uncover the impact of your human variants on disease risk, gene regulation, and protein function.
  • Remove biologically irrelevant mutations and reduce the amount of mutations you have to investigate.
  • Identify novel mutations not previously reported in the literature.
  • Understand gene regulation changes in your variants by mapping novel mutations to known or predicted regulatory sites.
  • Find disease genes, drug targets, and pathways linked to your variations.

Register for HGMD

  • You must register to login to HGMD
  • To request a login use Ask Librarian or email Jeremy Kupsco (jkupsco@emory.edu).
  • Logins are for use by Emory Employees only.
  • Please log off at the end of each session to prevent blocking other users' access.

To log into HGMD click here.


DNASTAR Lasergene is licensed by the Woodruff Health Sciences Center Library and is now offered at no cost to the Emory Research Community.  The Lasergene Core Suite includes full access to SeqBuilder, SeqMan Pro, MegAlign, MegaAlign Pro, GeneQuest, Protean Protean 3D, SeqNinja, Genvision, Primer Select and EditSeq.  Additionally, Seqman Ngen, Arraystar and Qseq are licensed for use by Emory researchers.

Technical Requirements

  • Most DNASTAR Lasergene products are available for both Windows (Windows XP, Vista, or 7) and Mac (OS 10.6 or later).
  • Array Star and QSeq are available only on the Windows platform (available for Mac when running a Windows 7 parallel desktop).
  • Please be aware that newly available modules SeqMan Ngen and Qseq require potentially large amounts of RAM.  A minimum of 8GB RAM for Qseq and a minimum of 16GB RAM for SeqMan Ngen are recommended.
  • The WHSC Library has available two computer workstations that can run SeqMan Ngen and Qseq in the library.

Registering and Downloading Lasergene

  1. Start by submitting a request to Ask A Librarian or contact Jeremy Kupsco (jkupsco@emory.edu)  to receive the IP address for the Lasergene Server at Emory.
  2. After obtaining IP address, download the appropriate version of Lasergene from Emory Software Express
  3. Follow the install prompts.
    1. Choose “silent install" to keep prompts to a minimum.   
    2. When DNASTAR Lasergene Authorization prompt pops up, choose the applications you wish to authorize and click next.  
    3. When prompted, select “Network” for License Type and use the provided server address to authenticate the download.

Off Campus Access

Lasegergene gives you the option to “checkout a temporary license for up to 30 days" that will allow off campus access, you can set this option up by clicking on “Commuter License Manager.”
MetaCore™ is an integrated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, proteomics, metabolomics, Co-IP pull-out and other custom interactions. MetaCore™ is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways for human, mouse and rat, supported by proprietary ontologies and controlled vocabulary. The analytical package includes easy to use, intuitive tools for search, data visualization, mapping and exchange, biological networks and interactomes.

Login To GeneGo MetaCore

Click here to login to GeneGo MetaCore

  • You must register to login
  • To register use Ask a Librarian or email Jeremy Kupsco at (jkupsco@emory.edu).
  • You will recieve an email form GeneGo with your login information.
  • Logins are for use by Emory Employees only.
  • Please logoff at the end of each session to prevent other users' access from being blocked.

Specialized Software Lab

Quantitative Software | Qualitative Software | Productivity Software | Geospatial Software

Overview

The Woodruff Health Sciences Center Library leases a number of software analysis tools that are essential to health sciences research. The software can be found in the Specialized Software Lab, located on the Plaza level of the WHSC Library. The lab features 4 PCs. Access to these computers is limited to individuals with an Emory netID and password. Priority is for those using the specialized tools.

Quantitative Software

Epi Info 7 Epi Info is a tool for data collection, analysis, visualization, and reporting using epidemiologic methods 
MATLAB MATLAB is a data visualization and analysis tool used in engineering and the sciences
R R is a programming language and open source software program used for statistical computing and data visualization
SAS SAS is a command-driven, quantitative program used for data management, visualization, reporting, and statistical analysis
SPSS SPSS is a menu-driven program used for data management, visualization, and statistical analysis
Stata Stata is a command/menu-driven program used for data management, visualization, and statistical analysis 

Qualitative Software

MAXQDA MAXQDA is a qualitative content analysis program used to evaluate and interpret textual, audio and video data
NVivo NVivo is a qualitative program for mixed methods research designed to collect, organize, and analyze content from interviews, surveys, audio files, and websites

Productivity Software

Access Database management software created by Microsoft
Excel Microsoft Excel is a spreadsheet application designed to collect, organize, manipulate, visualize, and analyze data
PowerPoint Software to create presentations with advanced audio and visual capabilities. Part of Microsoft office package
Word Word processor created by Microsoft
Visio Software for advanced, interactive diagramming. Standard, professional, or premium Office packages available

Geospatial Software

ArcGIS Mapping and spatial analysis software. One year trial available for students