2025 Archive
Alphafold Workshop with Guillaume Lamoureux (Virtual, link provided after registration)
Participants are expected to watch the prior AlphaFold workshop in advance.
May 14 12:00pm-1:30pm
May 28 12:00pm-1:30pm
Student Consultants: Jahmal Ennis
Registration will close May 7
Workshop Description:
Since its debut less than five years ago, AlphaFold has redefined structural biology—and it’s only the beginning. In this two-part workshop, Dr. Guillaume Lamoureux will dive into AlphaFold, ESMFold, and the broader impact of AI-powered tools on the future of research. Come explore how these systems work, what they can (and can’t) do, and how they’ll shape scientific discovery in the years to come.
Learning Goals
• Understand how AlphaFold and related models function and their limitations
• Explore how these tools integrate with general AI systems like LLMs
• Reflect on the evolving nature of scientific research in the AI era
Open to all STEM graduate students
OARC GitHub Workshop (In-person in JHSC 104BC) Hybrid option available. For the best learning experience we recommend attending this workshop in person.
- Beginner – March 5 12:00pm-2:00pm (Register for Introduction to GitHub Workshop)
- Intermediate – April 30 12:00pm-1:30pm (Register for Intermediate GitHub Workshop) Registration will close April 23
- Student Consultants: Shriya Subedy and Lindsey Riggs
Open Forum on Machine Learning and AI Advancements: Concerns, Opportunities, and Applications with Iman Dehzangi (In-person at JHSC 104A with Hybrid option)
- Apr 23, 12:00 pm-1:30 pm
- Student Consultants: Alyssa Vanerelli
Workshop Description:
The rapid advancements in machine learning (ML) and artificial intelligence (AI) are transforming diverse domains, from healthcare and education to finance and entertainment. This forum invites an open discussion on the implications of these technologies, exploring their transformative potential alongside ethical and societal concerns. Key topics include the role of AI in addressing global challenges with a focus on disease diagnosis, bioinformatics, and computational biology. Concurrently, we will address pressing issues like bias in AI systems and data privacy. Attendees are encouraged to share insights, challenges, and visions for the future.
Join an open discussion on the advancements of machine learning (ML) and artificial intelligence (AI), their implications, and their transformative potential across various sectors. We will discuss the role of AI in global challenges, particularly in disease diagnosis and bioinformatics, alongside ethical and societal concerns.
Learning Goals:
- Discuss concerns, opportunities, and ideas surrounding ML and AI.
Open to any STEM trainee.
Registration will close after April 16
Keeping up with the Scientific Literature with Anthony Geneva (In-person only at JHSC 104BC)
- Mar 26, 12:00 pm-2:00 pm
- Student Consultants: Jesse Sandberg
Workshop Description:
This workshop will combine lecture and hands-on practice into a single 2-hour session. Roughly the first half will consist of an interactive lecture providing an overview of strategies for finding and evaluating the relevance of scientific papers as well as a discussion of the difference between active and passive literature searching. The hands on portion will consist of a (very) brief example of active literature searches followed by an interactive demonstration of the construction of literature alerts and bots for the remainder of the session.
Learning Goals:
- Understand literature searching and archiving tools available to RU affiliates.
- Learn to rapidly evaluate the relevance of the papers discovered via these searches.
- Build automated tools for literature discovery.
- Understand passive vs. active means for discovering literature.
Open to any STEM trainee.
Registration will close after March 19
Code Review with Sunil Shende (In-person at JHSC 104BC)
- Mar 12, 12:00 pm-2:00 pm
- Apr 8, 2:00 pm- 4:00 pm
- Student Consultants: Ezry Santiago-McRae
Workshop Description:
This workshop focuses on reviewing Python (or similar programming language) code to encourage best practices for documentation, linting, and refactoring. Students will submit code samples with specific questions for critique, and in the second session, they will incorporate feedback to improve their code.
In the first session, students are asked to submit code samples along with specific questions they may have about the readability or efficiency of their code. This code is reviewed and critiqued by me and to the extent that time allows, by students attending the workshop. The critiques provide an opportunity to discuss general aspects of
best practices for code organization, documentation and layout. Students are given specific feedback for improving their code with the understanding that they will make those changes before the second session. These suggestions can include learning to use tools for documenting and testing the code.
In the second session, students return having incorporated the suggested corrections to their earlier code. The code is reviewed again and any additional suggestions for implementing good STEM-specific software engineering principles are reiterated and reframed based on the quality of the code.
Learning Goals:
- Learn to document code properly and use a linter to detect errors.
- Implement best practices in code organization, refactoring, and testing.
Open to any STEM graduate student.
Registration will close after March 5.
Surviving your PhD Qualifying Exam with Grace Brannigan (In-person at JHSC 104BC with Hybrid option)
- Feb 5, 12:00 pm-2:00 pm | JHSC 104BC
- Apr 9, 12:00 pm-2:00 pm | JHSC 104BC
Workshop Description: This two-hour workshop will present “survival tips”, cover expectations for the overall format, host multiple Q&A panels with students who recently qualified, give you a glimpse into the conversation when the student is out of the room, provide tips on answering questions, and help you construct your own checklist and timeline for the months leading up to the qualifying exam.
Learning Goals:
- Participants will increase their understanding of the experience for the written proposal, oral exam, and overall qualifying process.
- Participants will be able to prepare for their qualifying exam more systematically, with a planning toolbox and set of concrete steps.
- Participants will feel less of the “stress of the unknown” and gain confidence in their ability to grow and success in the qualifying exam process.
- Participants will gain perspective on what success “looks like” to the student, the PI, and the committee.
Open to any STEM graduate student. Pre-Qualifying CCIB PhD students are highly encouraged to attend.
Registration is now closed.
Data Interpretation with Andrey Grigoriev (Virtual)
- Feb 26, 12:00 pm-1:00 pm
- Apr 2, 12:00 pm-1:00 pm
Workshop Description: This workshop will help trainees interpret the results of their studies. Students will submit a brief description of their research problem two weeks before the first session, providing technical details needed for data interpretation. A subset of submissions (3-5) will be selected for detailed discussion, with suggestions on follow-up studies. In the second session, results from follow-up studies will be discussed.
2024 Archive
Intro to Python Programming (2-part workshop) In-person hosted by Software Carpentry Instructors
Dates: September 12 and 13 (2:00 PM-6:00 PM)
Location: JHSC 104BC
Are you an experimental student who wants to break their dependence on excel for plotting? Are you a new student rotating in a computational lab? This workshop is designed to cover the basics of programming in Python, with a special emphasis on manipulating data and plotting. Over the course of 8 hours (spread across two days) we will cover how to use a Jupyter notebook, variables and assignment, data types and type conversion, built-in functions and how to get help, libraries (numpy, pandas, and matplotlib), data manipulation, and plotting. This workshop is led by Software Carpentries certified CCIB student instructors.
This is a 2-day in person workshop in JHSC 104BC September 12 and September 13 from 2pm-6pm
Location: 201 S Broadway Camden, NJ 08103
Code Review with Testing hosted by Sunil Shende (2-part workshop) In-person
Dates: September 18 JHSC104A (11:20 AM-12:20 PM) & October 9 104BC (11:20 AM-12:20 PM)
Code Review is best suited for those with intermediate coding skills who have taken at least 2 computer science courses or have 1 year of research experience. Code Review will be held in 2 parts, if registering for this workshop you should plan on attending both sessions.
If you are planning on attending please join the #code_review channel on CCIB Slack and email Dr. Shende the following prior to the workshop:
- the specific snippets that we will be reviewing
- any specific reasons why you want the code to be reviewed
- which aspects of code review you would like addressed (documentation, linting, appropriate use of APIs
- testing issues; code opacity etc.
Scientific Figure Makeover Workshop hosted by Guillaume Lamoureux (2-part workshop) Virtual
Dates: September 25 & October 16 2024 (11:20 AM-12:20 PM)
Location: Virtual (Zoom)
Dates:
September 25 11:20-12:20pm
October 16 11:20-12:20pm
This is a 2 part workshop. If you are registering you should plan on attending both sessions to get the maximum benefit from this workshop.
The “Figure Makeover” workshop provides participants with an opportunity to present a figure they are currently preparing for publication, to discuss the presentation/communication challenges they are facing with it, and to receive feedback from their peers and from the instructor. (We will discuss as many figures as time allows. Complex/problematic figures welcome!)
Learning Goals for this workshop:
– Students will become more aware of what is required from a publication-quality figure and of what makes a figure effective at communicating information
– Students will practice providing/receiving feedback to/from their peers
iJOBS Career Panel: Non-research careers with a PhD hosted by Janet Alder Hybrid
Date: October 10 (12:45pm-1:45pm)
Location: JHSC 104BC
Your PhD can take you in many different directions, some of which you may have not even considered! Come meet a panel of Rutgers graduate school alumni to learn how they each took skills obtained in their PhD program and apply them in science-related careers including non-profits (Melissa VonDran), equity research (Lauren Timmins), consulting (Courtney Grady), medical communications/consulting (Juan Valdez Cappuccino), and patent law (Danielle Kozlowsky). There will be networking opportunity for those who attend in person.
Machine Learning with application in Bioinformatics hosted by Iman Dehzangi Hybrid
Date: October 23
Location: JHSC 104BC (11:00 AM-1:00 PM)
Introduction to Machine Learning (with applications in Bioinformatics) with Dr. Iman Dehzangi (Computer Science Professor and CCIB Member)
Nowadays we hear a lot about Machine learning and its application in different fields. It is widely considered as the most important force in advancing the technology and science. Yet, what is machine learning, how it is implemented, or how it actually works are not clearly explained. Here, I am going to present an introduction to machine learning. I will also present how it can be used to tackle some of the challenging problems in Bioinformatics and computational biology. We will also try some hands-on experience using Scikit-Learn library in python.
The learning goals of this workshop are to provide students with an introduction to machine learning, how it works, and how to move forward and learn more.This workshop is open to all STEM students. In-person and hybrid options are available.
Inferring Phylogenies hosted by Anthony Geneva (2-part workshop) In-person only
Date: October 30 JHSC104A & November 13
Location: JHSC 104BC (11:20 AM-12:20 PM)
In this workshop, students will be given a brief background on phylogenetics theory and Bayesian phylogenetic analyses. Next, students will work through a toy example of performing a basic phylogenetic analysis using provided data. Finally, students will perform an analysis on data they collect (or compile from public databases) and learn to interpret their results.
The learning goals of this workshop will focus on:
- Introduce students to the core concepts of Bayesian Phylogenetics
- Prepare data to analyze
- Perform a basic phylogenetic analysis as a group
- Perform and interpret a more advanced phylogenetic analysis of data compiled individually.
This workshop is best suited for intermediate computational researchers with at least a year of research experience or 2 have taken at least 2 computer science courses.
Flashtalk Feedback hosted by Grace Brannigan (2-part workshop) In-person
Dates:
November 20 11:00 AM-1:00 PM, JHSC 104BC
December 4 11:00 AM-1:00 PM, JHSC 104BC
This is a 2-part workshop. Participants should plan on attending both workshop dates (in-person) to get the maximum benefits of this workshop.
In this workshop, participants will practice and refine 3-minute “flashtalks” on their research for a general scientific audience. Participants should have a draft of their talk already complete at the beginning of the workshop.
Learning Goals:
1) Students will become more comfortable and confident while delivering a short format “flashtalk” for a general scientific audience
2) Students will practice providing meaningful and actionable feedback to each other
3) Students will learn to refine the content of their flashtalk to address feedback
Software Carpentries: Data Analysis and Visualization in R
Dates: October 15 and October 16 1:30pm-3:30pm in JHSC 104BC (2 part in-person workshop hosted in JHSC)
Have you ever wanted to upgrade your data visualization skills? Come to the R workshop! In this two-session, two-hour workshop, we’ll guide you through the basics for of R and RStudio, teach you how to wrangle messy data with dplyr, and make publication-quality graphics using ggplot2. This workshop will be hands-on, interactive, and hopefully you will feel more confident and excited to use your new skills to make extremely customizable graphs that go beyond the power of Excel!
The workshop will be in person only hosted in JHSC.
Learning Goals for the workshop are:
- Students will learn how to navigate R/RStudio.
- Students will understand the different data types in R and will learn how to manipulate them.
- Students will learn how to “wrangle” data with the “dplyr” package.
- Students will learn how to create publication-quality graphics using the “ggplot2” package.
Individual Development Plan Workshop hosted by Guillaume Lamoureux (Virtual)
Dates: November 4, 2024 (12:45 PM-1:45 PM)
Location: Virtual (Zoom)
Description:
Individual Development Plans (IDPs) and Mentorship Plans are now required for certain types of funding, making it more important than ever for students to create and maintain a clear career development strategy. Whether you are considering a career in academia or industry, an IDP can help you define and achieve your professional goals. myIDP, a free web-based tool, was created to support graduate students and postdocs in the sciences with career planning and goal-setting.
This workshop will guide you through using myIDP to build a personalized roadmap based on your strengths, interests, and goals. PIs are highly encouraged to recommend this workshop to their students, especially those seeking or currently receiving grant funding.