Basic Research Software

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

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

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 is an Electronic Lab Notebook (ELN) application. It’s used in the lab to efficiently organize research data, collaborate and share information, and streamline communication. It is an intuitive electronic notebook that allows users to log data by adding text, protocols, drawings, images, and tables as well as setup sample types, storage units, and other relevant experiment sample information. eLab includes regulatory and compliance features such as electronic signatures, audit trails, and FDA compliance.

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 Windows, EndNote X9 for Mac, EndNote X8, EndNote 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 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 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 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.

GPT4DFCI, a private, secure, HIPAA-compliant generative AI tool based on GPT and o1 models, is now available to Dana-Farber workforce members to try out for work purposes, excluding clinical care.

To request access:

1. If working remotely, be sure you're connected to VPN.
2. Visit the Informatics & Analytics GPT4DFCI sign-up page.
3. Log in with your MGB username and password.
4. Complete and submit the ticket.
5. Once your access is granted, visit https://gpt4dfci.dfci.harvard.edu 

Please review Dana-Farber’s new policy on acceptable use of generative AI. Workforce members are required to use generative AI systems in a manner that maintains the protection of protected health information (PHI), personally identifiable information (PII), and other confidential information. It also must be used in a manner that maintains the integrity required for scientific analysis as well as generation of scientific content such as text, images, graphics, and figures.

Please remember, publicly available AI tools can pose significant privacy and security risks. For this reason, only Dana-Farber-approved AI tools can be used for work purposes.

Do you want to discuss an idea for a custom GPT? Would you like API access? Get in touch.

More information: GPT4DFCI Press Release.

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

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 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:

• Jupyter Notebooks: https://jupyter.org/
• Python: https://www.python.org/
• “R”: https://www.r-project.org/

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 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.

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 licenses are obtained by submitting an IS Service Desk request.

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.