Course Structure

The key elements of the program are:

  1. A three week didactic and practical course at the University of California, Irvine, including
    • An initial preparatory week, 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
    • A two-week core course involving both lecture and 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.

Timeline of participant activities

1. The “prep” week

About a month 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); a reading list; licensed copies of Mathematica and MatLab software, along with installation instructions for additional open-source tools; and access to advanced training sets available via the course website. Upon arrival at UCI, they begin “preparatory” workshops, the goal of which is to bring participants “up to speed” in either mathematics, statistics and computation—through lectures and hands-on tutorials 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.

Participants will be assigned to one of the two prep-week courses according to their backgrounds. The Math and Computational Biology prep week 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. Tutorials will be run by a faculty lecturer with the aid of graduate student assistants. In the Foundations of Biological Sciences prep week, lectures each morning will introduce essential concepts in molecular biology, biochemistry, cell biology and development, followed in the afternoon by practice in core laboratory skills, such as nucleic acid based protocols, quantitative analytical methods (qRT-PCR, mass spectrometry), tissue culture manipulations (transfection techniques) and introduction to working with model organisms (chick/frog embryos, hydra, C. elegans, Drosophila). At the end of prep week, on Saturday, the two groups will merge to participate in Match Day and career mentoring activities that are described in detail in the subsequent Mentoring section.

Mathematical and Computational Biology Prep Week
AM PM
Mon Intro to Systems Biology
Calculus and Linear Algebra Review
Tutorials (Matlab-based)
Tues Dynamical Systems Tutorials (Matlab-based)
Wed Partial Differential Equations Tutorials (Matlab-based)
Thurs Biological statistics and fundamentals of informatics Tutorials (Matlab and R-based)
Fri Modeling with Mathematica Numerical Methods with Mathematica
Sat Match-Day: interdisciplinary collaboration
Career Opportunities & Panel Discussion
Foundations of Biological Sciences Prep Week
AM PM
Mon Intro to Systems Biology
Essential Molecular Biology
Foundational lab skills for biology; biochemistry tools
Tues Essential biochemistry Core molecular biology skills (lab)
Wed Essential Genetics Core bioinformatics skills (lab)
Thurs Essential Cell Biology Core cell biology skills (lab)
Fri Essential Developmental Biology Model developmental organisms (lab)
Sat Match-Day: interdisciplinary collaboration Career Opportunities & Panel Discussion

2. The “core course”

The content of the next two weeks, the “core 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.

Week 2 AM PM
Mon

Conceptual Toolkit for Systems Biology: Core Reactions and Combinations.

Genomics/Transcriptomics/Bioinformatics

Philosophy of Science

*Lab Module A: Modeling Biological Systems

Tues

Conceptual Toolkit for Systems Biology: cont’d

Genomics

*Lab Module A: Modeling Biological Systems
Wed

Synthetic Biology

Dynamical Behaviors

Project Development Day

Time for collaborative project development

Thurs

Biomechanics

Fluorescence Microscopy & Imaging

*Lab Module B1 or B2 (choice of 2 day module)
Fri

Morphogenesis & Patterning

Modeling Spatial Phenomena

*Lab Module B1 or B2 (cont’d)
Sat

Match Day Presentations (round 1)

Presentations of student projects;
Mentor and peer critique

Career Development Skills

Case studies: faculty, MCSB student forum;
Interdisciplinary grants and communication

Sun  Free day

 

Week 3 AM PM
Mon Gene Regulatory Networks (GRNs)
Mathematical modeling of GRNs
*Lab Module C
Tues

Growth Control

Multi-scale Modeling

*Lab Module C (cont’d)
Wed

Engineering Development

Primer on stochastics, populations and distributions

*Lab Module D1 or D2 (choice of 2 day module)
Thurs Project Development DayTime for team project development
Individual mentoring
*Lab Module D1 or D2  (cont’d)
Fri Match Day Presentations (round 2)
Mentor and peer critique;
Individual student plans for post-course mentorship;
Outline goals for next year

Mentoring Day and Career-Booster Award Competition

(begins in 2019 for alumni from 2018)

Sat Southern California Regional Systems Biology Conference (February 9th, 2019)

*Laboratory modules (tentative titles and instructors):

A: Modeling Biological Systems (Bardwell)
B1: Probing Membrane Receptor Dynamics through Imaging (Allard, Digman, Gratton)
B2: Synthetic Biology: Directed Evolution (Liu)
C: Gene Regulatory Networks in Early Xenopus Development (Cho, Mortazavi)
D1: Gene-Regulatory Control of Drosophila embryo patterning (Wunderlich)
D2: Single Cell Gene Expression of Tumor Heterogeneity (Andersen, Atwood, Nie)

 

3. Mentoring and career development activities: Match day presentations, panels and discussions

Within the three-week course, several days are allocated for mentoring and career development activities. The first of these begins on Saturday morning of the prep week, 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 throughout week two of the course. At the end of that week (Saturday morning) 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 third week, they can deliver an improved “pitch” to the other participants and faculty, who will again provide feedback.

In addition, one day each week will focus on career skills development and career opportunities. Saturday afternoon of the prep week will feature a panel on opportunities in academia, medicine, industry and government, with panelists including UCI faculty, recent graduates, and other professionals. Saturday afternoon of the following week will feature 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:

Option 1: They will more fully develop an interdisciplinary project into a detailed proposal that could potentially compete for seed funding in an appropriate venue. This could be something that emerges from the Match Day exercise, but need not be. It should involve one or more collaborators from another discipline, but those need not be other course participants. The main restriction is that the project be something new, involving the need for participation from outside participant’s current research discipline. Participants choosing this option will meet with the program directors on the final Friday of the course to discuss preliminary plans, and will identify a mentor from the course faculty, with whom they will be asked to follow up on a regular basis, through email and videoconferencing. Participating mentors will be expected to provide guidance on project development including, if appropriate, suggestions for potential collaborators/consultants and assistance in contacting such individuals. Mentors will also critique the written proposals that the trainees ultimately develop.

Option 2: They will write a fellowship application in which they propose to engage in interdisciplinary research. The proposal will depend upon the training level of the participant, but could include an NIH K25 proposal (Mentored Quantitative Research Development Award), other sorts of NIH K-proposals, an NIH F32 proposal, or an NSF Graduate Research Fellowship proposal. Participants choosing this option will meet with the program directors on the final Friday of the course to discuss their plans, and identify a mentor from the course faculty with whom they will be asked to follow up on a regular basis, through email and videoconferencing. Participating mentors will be expected to provide guidance on application preparation, focusing on effective communication of rationale and justification for interdisciplinary research. Whenever feasible, participants will be encouraged to submit their proposals to the appropriate funding agencies.

Course faculty who serve as mentors in this capacity will also make themselves available to address any career-related questions that their mentees may pose along the way, and will be encouraged to refer mentees to other colleagues who might serve as useful career contacts.

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

For those course participants who choose Option 1, return to present at the one-year mark, are U.S. citizens or permanent residents, and are interested in actually undertaking the interdisciplinary project that they have proposed, we’ve made available a small pool of funds to allocate for “Career Booster Awards”. These small awards (typically up to $4,000) will be made available in the form of funds to cover specific outsourced activities such as DNA sequencing, antibody preparation, transgenic mouse services, mass spectroscopy, cloud computing fees, or other one-time, services that could be directly invoiced to UCI. Although the amount of money is relatively small, our experience indicates that for trainees at the student or postdoctoral level such awards can be highly motivating.

Participants who receive Career Booster Awards will continue to be mentored and be expected to return to UCI once again at the two-year mark, both to attend the final Friday presentations, and to present a progress report on their interdisciplinary project in a special section of the SoCal Regional Conference on Systems Biology.