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A Short Course in

Systems Biology - Foundations

2021 Update

 

The August 2021 mini-course adapts elements of the original course for the virtual (Zoom) setting.  The first week introduces preparatory material designed to help those with primarily “wet” (e.g. molecular biology, cell biology, genetics, biochemistry, physiology, etc.) or “dry” (mathematics, physics, engineering or computer science) backgrounds catch up to each other.  The second week covers selected current topics in Systems Biology.  Career development and mentoring activities occur during both weeks. Please see the schedule for the mini-course below.

* All course activities will take place between the hours of 9:00am - 12:30pm PDT (12:00pm - 3:30pm EDT).

Week 1MathBio
MonIntro to Systems Biology; Standards and options in software for math and computationIntro to Systems Biology; Molecular biology
TuesDynamical systems; Mathematica tutorial; Math modeling and PDEsGenetics; Developmental biology; Cell biology
WedPanel; mentoring networkingPanel; mentoring networking
ThursControl of cell growth; Genomics; bioinformatics
FriPrinciples of evolution; Big data; Mentoring session

Week 2 
MonMachine learning & AI; Career skills workshop
TuesscRNAseq fundamentals; scRNAseq applications; scRNAseq challenges
WedSystems genetics; Synthetic biology; Mentoring session
ThursBiophysics and the microbiome; GWAS, genomics, scATACseq, ENCODE; Mentoring session
FriSuper-resolution imaging; Single molecule approaches; Mentoring session

Course Structure (resumes 2022)

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.
fasb-diagram

1. The “prep” week

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.

Math and Computational Biology

Prep Week

 AMPM
MonIntro to Systems Biology; A Selective History of BiologyTutorials (Mathematica -based); Match Night
TuesCalculus Review; Dynamical SystemsTutorials (Mathematica -based); Match Night
WedPartial Differential EquationsTutorials (Mathematica-based)
ThursBioinformatics; Modeling with MathematicaBioinformatics Tutorial
FriBig Data Analysis and Fundamentals of BioinformaticsBig Data Analysis Tutorial
SatParticipant PresentationsIntro to Project Development; Project Brainstorming; Grants and Grantsmanship

Foundations of Biological Sciences

Prep Week

 AMPM
MonIntro to Systems Biology; A Selective History of BiologyFoundational lab skills for biology (lab); Match Night
TuesEssential Molecular BiologyCell and molecular biology techniques (lab); Match Night
WedEssential Cell BiologyBioinformatics skills (lab)
ThursEssential GeneticsMolecular biology skills (lab)
FriAdvanced Essential Cell BiologyModel developmental organisms (lab)
SatParticipant PresentationsIntro to Project Development; Project Brainstorming; Grants and Grantsmanship

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.

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:

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.

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