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A Short Course in

Systems Biology - Foundations

Course Structure

The key elements of the program are:

  1. A four-week didactic and practical course offered online and at the University of California, Irvine, including:
    • An initial two weeks online, devoted to filling in gaps of knowledge or understanding in trainees who have either “Wet” (e,g. molecular biology, cell biology, genetics, biochemistry, physiology, etc.), or “Dry” (mathematics, physics, engineering or computer science) disciplinary backgrounds and lectures on relevant systems biology topics.
    • A two-week in-person course involving both lecture and hands-on laboratory modules.
    • Activities focused on teaching collaborative skills, including practical exercises and assessment.
    • Activities focused on career development.
  2. A post-course year during which participants receive long-distance mentoring to help them develop either an interdisciplinary fellowship application, or a new interdisciplinary research project.
  3. A return visit to UCI to present the results of the activities of the post-course year.
  4. A limited number of “career booster” awards to seed the implementation of interdisciplinary research projects conceived during the post-course year.

1. The Two-week Online Workshop

Before the start of the course, participants will receive a pre-course survey (to assess baseline knowledge and student expectations for the course and their careers). The goals of the “Online Workshop" are two fold: first, to bring participants “up to speed” in either mathematics, statistics and computation—through lectures that introduce concepts and important software tools—or foundational paradigms in biology, highlighting areas where interdisciplinary approaches are anticipated to play a major role in the near future, and second, to introduce key topics in systems biology that highlight the importance of interdisciplinary approaches in solving biological questions. 

For the first week of the online workshop, participants will be assigned to one of the two tracks according to their backgrounds. The Math and Computational Biology track will focus on mathematical, computational and statistical fundamentals (calculus, linear algebra, mathematical modeling, basic bioinformatics, etc.), and on developing facility with commonly used software that will be exploited in the rest of the course. In the Foundations of Biological Sciences track, lectures will introduce essential concepts in molecular biology, biochemistry, cell biology and development. For the second week, the two groups will merge to take lectures on relevant topics in systems biology.  Participants enrolled in the full course will participate in Match Day and career mentoring activities, described in detail in the subsequent Mentoring section, throughout the online weeks.

Math and Computational Biology Track

Online Week 1 Sample Schedule

Day 1-Intro to Systems Biology
- Calculus Review
Day 2- Dynamical Systems
- Mathematica Tutorial
Day 3- Modeling and PDEs
- Modeling with Mathematica
Day 4- Dev-Ops and GIT for Systems Biology
- Biostatistics
Day 5- Data Science for Biologists
- Functional Genomics

Foundations of Biological Sciences track

Online Week 1 Sample Schedule

Day 1- Intro to Systems Biology
- Molecular Biology
Day 2- Molecular Biology Methods
- Essential Cell Biology
- Essential Genetics
Day 3- Developmental Biology
- Cellular Biophysics
- Cancer Biology
Day 4- Immunology
- Neuroscience
Day 5- Bioinformatics for Computational Biologists
- Mass Spectroscopy

Online Week 2 Sample Schedule

All Participants

Day 1- Intro to Interdisciplinary Research
- Tissue Engineering
- Machine Learning and AI
Day 2- Synthetic Biology
- Genomics: Single-cell Sequencing
- Models of Morphogenesis
Day 3- Hair Regeneration
- Genomics: Read Alignment
- Panel on Grants and Grantsmanship
Day 4- Biophysics of Microbiomes
- Invited Speaker
- Closing Remarks

2. The In-person Course @ UCI

The content of the next two weeks, the In-Person Course, is organized around selected systems biology topics in signaling, gene networks, imaging and synthetic biology. Although focused on topics within systems biology, the content is designed to highlight broad generalizable knowledge and skills for interdisciplinary research. Most lectures will take place in the morning and be immediately followed by lunchtime discussions with the lecturers. Participants will spend most afternoons performing a series of 1-2 day lab/tutorial modules, each of which focuses on the modeling and analysis of data in a different model system. Student learning in labs and tutorials will be facilitated by tutors—typically MCSB graduate students—who will provide on-the-spot personal assistance and answers to questions in addition to the course faculty/instructors. Evenings are generally unscheduled to leave time for participants to continue lab projects, work on their interdisciplinary proposals (see below) or for lectures or tutorials that may be added ad hoc, in response to participant requests or needs.

A sample two-week curriculum is summarized below. The actual curriculum may differ due to scheduling issues, and will be updated on this website as changes are made. If you have questions about whether specific lecture or laboratory topics will be offered, feel free to contact us.

3. Mentoring and career development activities: Match day presentations, panels and discussions (for full course participants only)

Within the four-week course, several days are allocated for mentoring and career development activities. These begin during the online workshop weeks, when directors Enciso and Lander will lead a discussion about collaboration skills, drawing upon their own experiences and those of their colleagues, and covering topics such as identifying what keeps collaborations going, breaking down disciplinary barriers, resolving conflicts, and assigning credit. This will be followed by “speed dating” sessions among the participants, where they will learn more about each other in short one-on-one encounters. Briefly, participants will be asked to match up into interdisciplinary teams of two or three (mixing Wet and Dry backgrounds) to come up with a feasible interdisciplinary research project, on any biological or biomedical question of their choosing, that they will later be asked to “pitch” to the course faculty and participants. The project need not be something that the participants have the means to accomplish on their own, but it should reflect the participant’s interests and should be the seed of an idea that could be developed further, perhaps with the help of additional collaborators. Teams will be paired up with course faculty who will provide advice and feedback on ideas during the in-person weeks. At the end of the first in-person week, they will present their ideas to the course faculty and participants, and receive direct mentor and peer critiques. Participants will then be tasked with revising (or replacing) their proposal over the next six days, so that on Friday of the fourth week, they can deliver an improved “pitch” to the other participants and faculty, who will again provide feedback.

In addition, there will be activities focused on career skills development and career opportunities. For example, there will be a panel on career opportunities in academia, medicine, industry and government, with panelists including UCI faculty, recent graduates, and other professionals. Additionally, there will be a panel on interdisciplinary case studies, presented by course faculty and graduate students, including MCSB students who have garnered “opportunity awards” (local, interdisciplinary seed grants similar in spirit to the “career booster” awards discussed below). Faculty will also discuss the NIH and NSF granting systems, and the opportunities and challenges afforded by MPI grants, and the recent NIGMS Team Science initiative.

4. Mentoring and career development activities in the post-course year

A unique feature of this program is that participants will return home from the three-week course with an assignment aimed to further their interdisciplinary training and career development. They may choose from either of two options:

5. Career development activities at the one-year mark

Trainees who complete option 1 or option 2 will be invited to return to UCI for the final two days of the following year’s course (starting in 2019, this course will be held in annually in January, rather than May). On Friday morning, they will listen to the Match Day presentations of that year’s course participants, and take part in the oral critiquing of those presentations. On Friday afternoon, they will present the results of their own activities in the previous year, sharing their experience with the current year participants (we have found these sorts of cross-year interactions among trainees to be very effective educational devices in our graduate program). On Saturday they will attend the Southern California Regional Conference on Systems Biology, which takes place on the last Saturday in January, at which they will be invited to present a poster. We recognize that not all participants will complete their post-course year task, or be willing to give a presentation on it. We currently estimate that about 50% of course participants will make the return trip to UCI at the one-year mark.

6. Career development activities beyond the one-year mark

The renewal application for the grant supporting this course is currently under review.  If the application is successfully renewed, the students from the 2024 course will have an opportunity to continue their mentoring activities beyond the course.

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