Boot Camp January 2022

9th Annual Interdisciplinary Quantitative Biology Winter Boot Camp

Sponsors: Rutgers Institute for Quantitative Biomedicine and RCSB Protein Data Bank (PDB)
Format: Online; Dates: January 10-14, 2022

Articles published from this Boot Camp: Nicotine, Cancer, and Addiction; Pyruvate Kinase M2; Non-Homologous End Joining Supercomplexes; Secretory Antibodies; HER2/neu and Trastuzumab; and Vascular Endothelial Growth Factor (VegF) and Angiogenesis.


Instructors​

  • Research Professor David S. Goodsell, Ph.D.  (Boot Camp Director, Institute Faculty Member)
  • University Professor Stephen K. Burley, M.D., D.Phil. (Institute Founding Director)
  • Associate Research Professor Shuchismita Dutta, Ph.D. (Institute Faculty Member)

Invited Speakers​

  • Maria Voigt - Graphic Designer/Software Developer, RCSB Protein Data Bank (Scientific Illustrator/Communicator)
  • James Sommers - Writer and Programmer based in New York, NY.

Who Should Participate:  Undergraduate (sophomores/juniors/seniors) and graduate students interested in science writing/visualization/communications for biology and medicine.
Both Rutgers Students and Visiting Students (by nomination/invitation only) are encouraged to participate.

Why You Should Participate: Successful participants will develop science communication skills, both the written word and 3D molecular visualization, by working closely with experts on writing projects that will produce content suitable for use by researchers, educators, students, and members of the curious public around the world. These skills will help you in your coursework, your research, and your career as you develop and mature as scientifically-sophisticated citizens important to the viability of our democracy.

What You Will Get Out of the Experience: Successful participants will be published scientific communicators! Your work will be published on the RCSB Protein Data Bank Education and Outreach website (PDB101.RCSB.org), which logged more than 800,000 unique users worldwide in 2020. You will be able to point to this accomplishment as you apply for graduate and professional schools, seek scholarships and fellowships, and pursue new career opportunities.

The Experience: The Boot Camp will be an intensive, immersive, hands-on learning experience spanning five full days (~8 hours/day). Participants will work in teams of three participants each under the direction of Boot Camp Instructors. All activities will be online.

The Value Proposition: Previous Institute for Quantitative Biomedicine Winter Boot Camps have changed the lives and benefited the careers of 100s of Rutgers students since we began offering this opportunity in January 2014. 

Our Creative Process: Each team will work together online to draft a new RCSB Protein Data Bank (PDB) Molecule of the Month (MotM) article destined for publication on PDB101.RCSB.org. Individual team topics will be selected from a list pre-determined by RCSB PDB leadership. To learn more about MotM, visit PDB101.RCSB.org .

Your Deliverables: Each team will produce a polished draft MotM article describing their selected topic, complete with literature references and illustrations.

Our Final Review Process:​ Draft MotM articles will be refereed by Boot Camp Instructors and subject matter experts.

Your Publications: Accepted MotM articles will be published on the PDB101.RCSB.org website with each responsible team member listed as a co-author together with David Goodsell. MotM articles will be citable on your resume and curriculum vitae using a unique Digital Object Identifier (DOI).

Learn More About  the Protein Data Bank:  The Protein Data Bank (PDB) is the global archive of three-dimensional (3D) biomolecular structure data . Founded in 1971 with just seven protein structures as the first open-access digital data resource in all of biology, the PDB today houses more than 180,000 structures of proteins, DNA, RNA, macromolecular machines, viruses, and virus-like particles. The US-funded RCSB Protein Data Bank (RCSB.org) integrates the entire corpus of PDB data with >50 external biodata resources, and provides easy-to-use web-based search and molecular visualization tools to assist many millions of PDB data consumers worldwide in finding, analyzing, and visualizing 3D structures of macromolecules and their complexes with one another, drugs, antibodies, enzyme cofactors, etc. In 2020, more than 5 million unique users directly accessessed the RCSB.org website. PDB data file downloads in 2020 numbered more than 1.3 billion.

Learn More About Molecule of the Month: The RCSB PDB MotM series edited and authored by ​ David S. Goodsell (RCSB PDB and The Scripps Research Institute) presents short accounts on selected molecules from the Protein Data Bank. Each article includes an introduction to the structure and function of the highlighted molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details.  In 2020, more than 800,000 individuals worldwide accessed PDB101.RCSB.org.

Schedule of Events January 10th-14th 2022

2022 IQB Winter Boot Camp Flyer

Monday January 10th 2022

Morning Session -- Basic Principles of Scientific Communication (Main ZOOM Room)
9:30 Orientation
9:45 Lecture: Choosing and Researching Topics for the Molecule of the Month (MotM)
10:00 Lecture: Writing a Molecule of the Month Article
10:30 Break
11:00 Lecture: Basics of Scientific Writing and Visualization
11:30 Lecture: Introducing Boot Camp Topics
11:45 Choice of research topic
12:00 Lunch

Afternoon Session -- Forming Your Team and Getting Started! (Main ZOOM Room)
1:00 Lecture: Being Successful in a Collaborative Team
1:20 Teams, research topics, and Mentor designations announced
1:30 Teamwork: Teams meet in ZOOM Breakout Room to choose team name and mascot *
1:45 Teamwork: Teams meet in ZOOM Breakout Room to do initial review of research topic *
2:00 Main Zoom Room Report Back
2:15 Break
2:30 Teamwork: Read articles for your work assignment *
3:30 Teamwork: Begin discussion of the story in Team ZOOM Breakout Rooms *
* During all Teamwork sessions, consult with your designated Mentor in the Mentor ZOOM Breakout Rooms pro re nata (prn)
4:15 Group check-in (Main ZOOM Room)
4:30 Break for the day

Tuesday January 11th 2022

In the morning, we’ll learn how to use the tools for finding and visualizing biomolecular structures, and in the afternoon, teams will create an outline of what they want to present in their articles.

Morning Session -- Tools Training (Main ZOOM Room)
9:30 Tutorial: Tools for finding structures in PDB: RCSB
10:00 Tutorial: Tools for visualizing structures in PDB: MolStar (aka Mol*)
10:30 Break
11:00 Tutorial: Tools for illustrating structures: Illustrator and Jmol
12:00 Lunch

Afternoon Session -- Developing Your Story
1:00 Plan and deliverables for the afternoon (Main ZOOM Room)
1:05
  • Teamwork: Explore structures that will motivate your story *
  • Teamwork: Additional literature searching to expand topic if needed *
  • Teamwork: Draft outline of major concepts in each section *
3:00 Break
3:15 Team Progress Check: Pitch Your Story (Main Zoom Room)
  • Format: short elevator pitch of your ideas for the story
  • Deliverable: slides or Word document with bullet points for each MotM section
  • Timing: 6’ for pitch plus 4’ for Q/A from other Teams
4:30 Break for the day

Wednesday January 12th 2022

We’ll start with a short presentation by a SciComm visual arts professional, and then we’ll spend the day working on our articles. By the end of the day, each team should have drafts of the images that will be included in the article, and an outline for the concepts that will be included in the article.

Morning Session -- Create Your Images
9:30 Plan for the day (Main ZOOM Room)
9:35 SciComm Professional: Maria Voigt “Best Practices in Visual Communication”
10:20 Deliverables and process for today’s work session
10:30 Break
10:45
  • Teamwork: Finalize PDB structures motivating your story and sketch ideas for figures *
  • Teamwork: Design images in consultation with David Goodsell *
12:00 Lunch

Afternoon Session -- Create Your Images (cont.)
1:00
  • Teamwork: Continue designing and refining images with David Goodsell *
  • Teamwork: Finalize story idea and integration with figures and begin outlining your article *
3:00 Break
3:15 Team Progress Check: Pitch Your Structures/Figures -- Main ZOOM room
  • Format: short elevator pitch of your ideas for figures
  • Deliverable: slides or Word document with draft figures for each MotM section
  • Timing: 6’ for pitch plus 4’ for Q/A from other Teams
4:30 Break for the day

Thursday January 13th 2022

We’ll spend most of the day writing the text for the articles and finalizing the figures. We’ll take a break from writing after lunch to hear from a professional scientific writer and journal editor. By the end of the day, each team should have a full draft of the text to share in the “Progress Check” session.

Morning Session -- Write Your First Draft
9:30 Plan and deliverables for the day (Main ZOOM Room)
9:35 SciComm Professional: James Sommers “Writing about Science to Engage and Educate” (Main ZOOM Room)
10:15 Deliverables and process for today’s work session
10:30 Break
10:45
  • Teamwork: Writing and revision of first draft *
    • Exchange of drafts w. team members
  • Teamwork: Finalize figures *
12:00 Lunch

Afternoon Session -- Write Your First Draft (cont.)
1:00 Teamwork: Writing and revision of a draft of the entire article *
3:00 Break
3:15 Team Progress Check: (3 breakout rooms)
Teams exchange full draft with another team for critique
  • 30’ to read drafts
  • 15’ discussion of one draft
  • 15’ discussion of other draft
  • 15’ review of learnings by both teams
4:30 Break for the day

Friday January 14th 2022

On the final day of the Boot Camp, we’ll finish the articles and get them ready for review and publication. The article should be finished by lunch time, so that we can share them with the other teams in the afternoon.

Morning Session -- Pull Everything Together!
9:30 Plan for the Day (Main ZOOM Room)
9:35 Teamwork: Consolidate edits to produce your final draft of the MotM article *
10:30 Break
10:45 Teamwork: Consolidate edits to produce your final draft of the MotM article *
12:00 Lunch

Afternoon Session -- Team Presentation of Molecule of the Month Articles!  (Main ZOOM Room)
1:00 Team Presentations: Formal presentation and critique for each MotM article
  • Format: Team members read aloud MotM sections
  • Deliverable: Full article with embedded figures in Word document
  • Timing: 10’ per team plus 10’ Q/A
3:00 Break
3:15 Debrief: Provide feedback to Mentors and complete Boot Camp survey
3:45 Plans for Peer Review/Final Round of Edits/Publication of MotM Articles
4:00 Close, Congratulations, Presentation of Certifications of Excellence!