MolSSI Intro
The Molecular Sciences Software Institute
A nexus for science, education, and cooperation for the global computational molecular sciences community.
Software Infrastructure
Education Initiative
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Industrial Training
Software Fellowship Program
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Education at the MolSSI

Education of students, post-docs, and faculty on programming and Best Practices in Software Development is a large part of MolSSI's mission. Our education program consists of our cohorts of Software Fellows, online training materials, and multiple workshops online and at various locations each year around the US.
Software Fellowships

Meet Our Fellows

The MolSSI continues to fund prestigious software fellowships that recognize advanced graduate students and postdocs pursuing the development of software infrastructure, middleware, and frameworks that will benefit the broader field of computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science.

MDAnalysis, in conjunction with the Molecular Sciences Software Institute(MolSSI) and with the support of the Chan Zuckerberg Initiative, and the Center for Biological Physics, is holding a free, 2-day workshop on June 24th-25th, 2024 at Arizona State University in Tempe, Arizona, USA.

This two-day workshop is designed to transform attendees from users to developers and will cover an introduction to MDAnalysis, software best practices, and guide participants through the creation of their own MDAKit.

MDAnalysis developers and experienced MolSSI instructors will teach participants how to build their own MDAnalysis-based Python packages by guiding them through the development of their own MDAKits. Specifically, the workshop will include 3 modules:

  1. An introduction to using and writing custom analyses in MDAnalysis;
  2. An overview of software development and maintenance best practices;
  3. An interactive hackathon session where participants write their own MDAKits.

Register by May 27, 2024 (midnight anywhere on Earth): Registration Link

For more information about the workshop, please visit the MDAnalysis website.

Join us for an engaging two-day workshop designed to teach programming and data handling skills using Python for people working in the molecular sciences and learn how to speed and enhance your learning using artificial intelligence. This event is ideal for students and professionals eager to get started with Python scripting and interested in leveraging AI tools like ChatGPT to learn coding faster and more efficiently. Participants can choose to attend either the Python basics session, the AI coding assistance session or both, with each day structured into two segments from 9:00 AM to 12:00 PM and 1:00 PM to 4:00 PM.

Date: August 17-18, 2024

Location: CU Denver campus (0.25 miles from Convention center where ACS convention is being held)

Local Organizer: Prof. Scott Reed

Capacity: 40 students

Registration Link

Workshop Agenda:

Day 1: Python Scripting Essentials
Lead Instructor: Ashley Ringer McDonald, MolSSI and Cal Poly San Luis Obispo

Kickstart your learning with an intensive dive into Python scripting, guided by Ashley Ringer McDonald. The day’s agenda is structured around getting students up to speed quickly with the basics of Python syntax and handling molecular files.

  • Morning Session:
    • Introduction to Python: Get to grips with the basics of Python syntax and set up your development environment.
    • File Parsing: Learn techniques to navigate and extract critical data from text files.
    • Processing and Writing Files: Extend your skills to handle multiple files simultaneously, enhancing your data processing capabilities.
  • Afternoon Session:
    • Working with Tabular Data: Discover methods to manage and analyze data in tabular formats.
    • Plotting and Data Visualization: Conclude the day by learning how to create impactful visual representations of your data.

Day 2: AI-Assisted Coding
Lead Instructor: Scott Reed, University of Colorado Denver

Day two shifts focus to the cutting-edge area of AI-assisted coding. This part of the workshop is dedicated to mastering Generative Pretrained Transformers (GPTs) such as OpenAI’s ChatGPT as a coding assistant, which will help participants enhance the efficiency and quality of their coding practices. Completing Day 1 provides sufficient background to attend Day 2 or those with prior coding experience can start with this material.

  • Morning Session:
    • Strategies and methods for using GPTs as a Coding Mentor: Learn best practices to use GPTs for generating, testing, and troubleshooting Python code throughout your process of learning to code. See how you can integrate AI tools into various coding environment.
    • Safety, Security, Ethics, and Avoiding Hallucinations: Gain insights on how to discern and handle potential inaccuracies in AI-generated material, how to identify copyrighted and license issues and what security vulnerabilities to be aware of when using GPTs.
    • Debugging Your Code with GPTs: Utilize AI to debug and refine your code and to better understand error messages and learn how to correct code based on GPT feedback.
    • Chemistry Python Package use through GPTs: Learn what tools you can expect a GPT to be conversant in and how to expand the knowledge of a GPT to meet your needs in coding for the molecular sciences. Learn how to use Python packages such as rdkit to benchmark and verify your results.
  • Afternoon Session:
    • Prompt Engineering: Develop skills to craft effective prompts that yield better results from AI when generating Python code. Learn about upcoming advances in code assistant tools. Learn tricks for avoiding lazy answers.
    • Pair Programming with ChatGPT: Experience how AI can act as a collaborative partner in code development.
    • Advanced AI Programming Support: Explore advanced techniques for leveraging AI for more complex coding tasks, learning new languages, integrating code within existing codebases, and managing larger projects.

Additional Information:
MolSSI will provide coffee and lunch for all participants. With a cap of 40 students, early registration is encouraged to secure a spot in this transformative workshop.

Whether you’re looking to enhance your foundational Python skills or eager to integrate AI into your coding practice, this workshop offers valuable insights and hands-on experience in both areas. Join us for an enriching educational experience that will expand your technical capabilities and prepare you for future challenges in the field of programming.

EDIT: We appreciate the great response we’ve seen to this workshop offering. We had capped the registration at 50 people to ensure that we can provide a high quality workshop to attendees, and we’ve already hit the registration limit. We are currently reviewing our personnel allocations for the workshop to see if we can expand and re-open registration. We will update this page and post a tweet if we are able to expand registration. 

MolSSI is pleased to announce that we will be holding an April webinar series on our Python Package Development Workshop. This workshop will be held over 2 weeks, with classes taking place on April 9, April 11, April 16, April 18, and April 19 from 1 PM to 4 PM ET (Eastern Time – the timezone of the Eastern United States) via Zoom.  This workshop series is offered at no cost to attendees.

Our best practices workshops introduce and promote MolSSI best practices to workshop attendees. In this course, students create a Python package using best practices and the MolSSI CookieCutter, write unit tests, create online documentation, and host this project on GitHub. The audience for this course is students or researchers who already regularly program in Python, but would like to learn how to start using version control, unit testing, and continuous integration in their projects. Prior programming experience is required to participate.

Classes will be held over Zoom, and each student should follow along with coding exercises on their laptop.

The Python Package Best Practices Course covers the following topics:

  • Conda and Python environments
  • Structuring a Python project using the MolSSI CookieCutter.
  • Version control using git
  • Python Coding Style
  • Online code repositories such as GitHub
  • Code collaboration and GitHub workflows
  • Unit testing and the PyTest testing framework
  • Code coverage
  • Continuous integration tools
  • Documentation for Python packages using Sphinx.

To sign up for the webinar, please fill out the registration here by April 5, 2024. You can see a tentative schedule here. Registration will be capped at 50 students.

If you missed the Informational Webinar about the MSF Program on March 1, you can access the Zoom recording via THIS LINK.

The Molecular Sciences Software Institute (MolSSI) is pleased to announce that the 2024-25 Software Fellowship competition is now open for submissions for ONE-YEAR Fellowships (from 1 July 2024 thru 30 June 2025). These prestigious Fellowships recognize advanced graduate students and postdocs pursuing the development of software infrastructure, middleware, and frameworks that will benefit the broader field of computational molecular sciences, including biomolecular and macromolecular simulation, quantum chemistry, and materials science. Recipients will have the opportunity to work with scientists at the MolSSI in order to implement recommended best practices, putting the Fellow’s project on a firm foundation. Fellows will receive specialized training in state-of-the-art software design principles and tools, and they will engage in outreach and educational efforts organized by the MolSSI.  Each Fellow will be assigned a mentor from among the Institute’s Software Scientists, who will oversee their software development efforts and training.  In addition, the 2024-25 Fellows will spend a week at MolSSI HQ (mid-July dates to be announced soon; Sunday PM through Friday PM) to interact with the Software Scientists during the “Software Best Practices Boot Camp.”

The MolSSI Software Fellowships will include a number of benefits:

Graduate Student Fellowships:

  • A generous stipend of $40k total for the 12-month Fellowships, plus tuition and required fees;
  • Travel allowances sufficient to fully cover visits to the MolSSI headquarters, as well as participation in MolSSI workshops or summer schools.

Postdoctoral Fellowships:

  • A generous stipend of $60k total for the 12-month Fellowship;
  • Travel allowances sufficient to fully cover visits to the MolSSI headquarters, as well as participation in MolSSI workshops or summer schools.

Note that MolSSI Fellowships are paid from NSF Participant Support funds. The only allowable expense categories are stipend, tuition and fees; F&A (indirect costs) and health insurance costs are not allowed.

Eligibility and Selection Criteria:

The MolSSI Software Fellowship program is presently limited to graduate students and postdoctoral associates at accredited U.S. academic institutions. Graduate student Fellows are expected to be enrolled full time at their home university, and postdocs must be fully employed or have an offer of full employment prior to acceptance of the award.  The MolSSI Software Fellowships are an equal opportunity program open to all qualified persons without regard to race, gender, religion, age, physical disability or national origin.  Awardees may accept other concurrent awards that do not require a significant time or service commitment.

MolSSI Software Fellows will be selected by the MolSSI Science and Software Advisory Board based on (1) the quality of the applicant’s software research proposal and its relevance to the Institute’s goals; (2) the applicant’s research productivity, including previous software-development efforts; (3) previous academic performance; and (4) external references.

Application Requirements:

A complete MolSSI Software Fellowship Application must include:

  • Project description (maximum of two pages, not including references);
  • Current curriculum vitae;
  • Undergraduate transcripts (graduate applicants only); graduate transcripts (all applicants);
  • Examples of previous software development products (e.g. links to source-code repositories or other code samples);
  • Two letters of support, one of which must come from the applicant’s current research adviser;

To receive full consideration for a Software Fellowship, all application materials (including letters of recommendation) must be submitted by April 1, 2024

Please complete the application and upload the required documents HERE.
Letters of recommendation should be uploaded separately by your references 

Inquiries to:

Additional Information:

  • Award Number (FAIN): 2136142
  • Award Instrument: Cooperative Agreement
  • Award Date: 07/30/2021
  • Award Period of Performance: Start Date: 08/01/2021 End Date:
  • Project Title: S2I2: Impl: The Molecular Sciences Software Institute
    Managing Division Abbreviation: CHE
  • Research and Development Award: Yes
  • Funding Opportunity: NSF 20-1 Proposal & Award Policies & Procedures
    Guide – PAPPG
  • CFDA Number and Name: 47.049 Mathematical and Physical Sciences

The Molecular Sciences Software Institute (MolSSI) is delighted to announce the launch of a new education and faculty development program: Accelerating Curricular Transformation in the Computational Molecular Sciences (ACT-CMS). The goal of ACT-CMS is to transform science curricula by accelerating the integration of programming and computation into existing molecular science courses through faculty training and the development of open and reusable curricular modules.  ACT-CMS is generously funded by the National Science Foundation’s Training-based Workforce Development for Advanced Cyberinfrastructure program.

The two-year Faculty Fellowship, which is the cornerstone of ACT-CMS, will be awarded to a molecular science educator developing curricula integrating programming and computation into existing science courses. Throughout the program, Faculty Fellows will receive curriculum development and assessment training and will upskill their programming and computational skills. They will produce a curriculum module that uses programming and computation to teach STEM concepts in an existing course that they teach. These modules will be open and reusable, allowing other educators to adopt them in their classrooms.

An ACT-CMS Faculty Fellowship offers the following benefits:

  • $3500 stipend each year of the fellowship.
  • $1500 travel funding each year of the fellowship.
  • Mentorship from an ACT-CMS Programming and Computation Mentor and an ACT-CMS Curriculum Mentor.
  • Annual meeting at MolSSI headquarters for training and networking.

Application window for the first cohort of Faculty Fellows will open 29 January 2024.
Inaugural Workshop: June 17-24, 2024, at MolSSI HQ in Blacksburg, VA

You will find full information and eligibility requirements at the ACT-CMS Website!

Fellows will be selected through a competitive application process. Applications will be accepted from 29 January through 29 February, 2024. Fellows will be notified of their selection in early April 2024.

We will have an online information session and Q&A about the program on January 29, 2024 at 10 am PT/1 pm ET.  Register for the information session here.

NVIDIA Deep Learning Institute (DLI) is conducting a series of free virtual workshops for academia and higher education in the North America. Join the MolSSI Industrial Training Program and our Software Scientist and Certified Instructor, Dr. Sina Mostafanejad for a hands-on Fundamentals of Accelerated Computing with CUDA C/C++ workshop on November 10 from 11:00AM-7:00 PM ET (8:00AM- 4:00PM PST)

You can stay up-to-date about the upcoming workshops by subscribing to our newsletter here.

MolSSI Workshops

The MolSSI’s Software Workshop program is a community-driven effort in which researchers from academia, industry, and national labs propose timely and important topics focused on the software needs of the molecular sciences, and the MolSSI organizes or facilitates the event.