Basic Research Software

Adobe: Acrobat, Photoshop, Illustrator

Institutions: DFCI

Access and support: Adobe request

DFCI now has an enterprise-level licensing for Acrobat, Photoshop, and Illustrator, direct from Adobe. More information can be found on DFCI Online here.
Having Adobe installation problems? Click here.

ChemDraw

Users: Basic researchers

Institutions: DFCI

Access and support: Installaton Instructions

ChemDraw is a molecule editor and chemistry communication suite for the transformation of chemical drawings into shareable chemical knowledge.

DNASTAR Lasergene

Genomic, structural biology, molecular biology, and cloning suite applications

Users: Basic researchers

Institutions: DFCI

Access and support: Installation instructions

The DNASTAR Lasergene package is the most robust software offering from DNASTAR and includes genomics, structural biology, molecular biology, and cloning suites applications.
You can find more training and tutorial information from the vendor tutorial library

eLabJournal: Electronic Lab Notebook (ELN)

Enter data, protocols, observations, notes, graphics, and much more using your computer or mobile device

Users: Basic researchers

Institutions: DFCI

DFCI is in the process of implementing an Institute-supported electronic lab notebook, eLabJournal. Further information will be posted on this site and communicated through the Research Communications Newsletters and various faculty meetings as the project progresses.

EndNote

Manage bibliographies, citations, references

Users: Basic researchers

Institutions: DFCI

Access and support: Installation instructions

EndNote is a product from Clarivate Analytics and is the industry-standard software tool for publishing and managing bibliographies, citations, and references. More information on EndNote can be found here. You can also find training materials on the vendor website: EndNote X9 for WindowsEndNote X9 for MacEndNote X8EndNote X7

Note: EndNote is not compatible with Dropbox or any cloud-sharing app, like Google Drive. Use EndNote Sync to create a version of your library in the cloud (see EndNote menu, Preferences, Sync). You can find more information on this and other topics at the EndNote community forums.

FileMaker Pro

Tool used to create custom apps

Institutions: DFCI

Access and support: FileMaker Pro 18 download

FileMaker Pro Advanced includes a set of advanced tools to help you design and develop custom apps faster and easier. Plus, you’ll get robust analysis capabilities, powerful diagnostic tools, and much more.
Partners offers FileMaker Pro free to clients as long as they host your database. 

Galaxy

Scientific workflow, data integration, and analysis

Users: Basic researchers

Institutions: DFCI

Access and support: Learn Galaxy

Galaxy is a scientific workflow, data integration, and analysis platform that aims to make computational biology accessible to research scientists who do not have computer programming experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system. To learn more about NGS Analysis with Galaxy and IGV, please visit RCApps.

GenePattern

Genomic analysis tools

Users: Basic researchers

Institutions: DFCI

Access and support: GenePattern

GenePattern is a powerful scientific workflow system that provides access to more than 220 genomic analysis tools. You can use the analysis tools as building blocks to design sophisticated analysis pipelines that capture the methods, parameters, and data used to produce analysis results. Pipelines can be used to create, edit, and share reproducible in silico results. For more information, please visit the Bioinformatics Service page.

GraphPad Prism

Scientific graphing, nonlinear regression, statistics, data organization

Users: Basic researchers

Institutions: DFCI

Access and support: Installation instructions

GraphPad Prism, available for both PCs and Macs, is a powerful statistical tool that combines scientific graphing, nonlinear regression, understandable statistics, and data organization.

Dana-Farber owns a limited site license, so the software is free to all DFCI users. There is a limit of one license per user on one computer. You can find training and tutorial materials from the GraphPad web site: Learn Prism.

If you are leaving Dana-Farber, you should uninstall Prism. How to uninstall Prism: Uninstall

If your computer is being transferred to another employee, you should deactivate your license, so the serial number is not associated with your old computer. You can install and activate Prism on your new computer. Deactivate Prism serial number: Deactivate

Lab Websites

Develop and maintain lab websites

Users: Basic researchers, Research staff

Institutions: DFCI

DFCI's Communications Department offers a Lab Website Program (LWP) at no cost, utilizing DFCI branded templates designed for non-technical professionals to learn and use.
Contact to get started: Luise Dittrich - Project Manager, LWP.

Matlab

MatLab will no longer be supported at the enterprise or department level

Matlab will no longer be supported and new licenses are not available. Existing licenses will be honored.
Here are some links to similar programming tools.  Please understand that we are not able to provide support for these applications and they are just suggestions for your information:

Qiagen Informatics Workbench

Qiagen Informatics Workbench contains CLC Genomics Workbench, CLC Biomedical Workbench, and CLC Main Workbench

Users: Basic researchers

Institutions: DFCI

CLC Genomics Workbench
CLC Genomics Workbench is designed to solve the data analysis challenges of high-throughput sequencing with high-throughput sequencing machines. CLC Genomics Workbench enables researchers to rapidly analyze and visualize large amounts of data generated by NGS machines. Its user-friendly and intuitive interface essentially takes high-throughput analysis solely from bioinformatics programmers doing command-line scripts, and opens it up to scientists searching for biological results. CLC Genomics Workbench incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of a typical NGS workflow. CLC Genomics Workbench supports key next-generation sequencing features within genomics, transcriptomics, and epigenomics, and includes all the tools of CLC Main Workbench. To learn more, visit the vendor website.

CLC Biomedical Workbench
CLC Biomedical Workbench offers flexible, ready-to-use analysis workflows. Its main features include the ability to quickly analyze complex data, modify or personalize workflows, filter and visualize your data, and compare results with relevant databases. Built upon the Genomics Workbench framework, this software has been optimized for use with samples from humans or a number of model organisms. To learn more, visit the vendor website.

CLC Main Workbench
CLC Main Workbench contains a variety of toolkits to work with DNA, RNA, and protein analysis. These tools include gene expression analysis, primer design, molecular cloning, phylogenetic analyses, and more. For a comprehensive list of features and capabilities, visit the vendor website.

Qlucore Omics Explorer

Visualize, QC, apply statistics, and create publication-ready graphics

Users: Basic researchers

Institutions: DFCI

Access and support: Qlucore

Qlucore Omics Explorer facilitates a dynamic, visualization-guided analysis of OMICs data, applicable to various phases of a discovery cycle. What differentiates Qlucore is the combination of speed, advanced analytics, seamless workflow, and simplicity. With Qlucore you can visualize, QC, apply statistics, and create publication-ready graphics, such as 3D Principal Component Analysis, heat maps, and various 2D plots. This tool suite empowers researchers to participate in their data analysis, exponentially shortening time to result and biological insight while improving accuracy of the findings.

Sequencher

Users: Basic researchers

Access and support: Installation instructions

Sequencher empowers the benchtop scientist by bringing the latest peer-reviewed NGS algorithms out of the command line and into an intuitive point and click interface. Whether performing reference-guided alignments, de novo assembly, variant calling, or SNP analyses, Sequencher has the tools you need to get results.  

Sequencher is product from Gene Codes. You can find useful training and tutorial information from the Sequencher training website.

UCSC Genome Browser

Interactive website offering access to genome sequence data

Users: Basic researchers

Institutions: DFCI

Access and support: Genome Browser

UCSC Genome Browser is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast, interactive performance. It is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of data at many levels. 

The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the UCSC Genomics Institute. For more information about Genome Browser, you can visit the UCSC website and FAQs. You can access the Genome Browser via DFCI gateway

Visio

Diagramming and vector graphics app often used to map workflows

Institutions: DFCI

Visio licenses are obtained by submitting an IS Service Desk request. Follow these instructions to place your request.
Note - The cost for a license is $9.72 per month. You will need to submit a cost center to charge against. 

Websites for research and clinical programs

Graphic design, content, programming, social media, and hosting

Users: Basic researchers, Clinical researchers

Institutions: DF/HCC, DFCI, Outside participating sites

DFCI’s Health Communication Core develops websites ranging from simple, static sites to complex, interactive web applications. The HCC creative team provides professional writing, graphic design, programming, social media, and strategy development services for:

  • Research recruitment/retention
  • Online interventions
  • Decision aid development
  • Research dissemination
  • Awareness and outreach

Contact health_communication@dfci.harvard.edu to explore how HCC can help strengthen your online presence.