Predoctoral Program
Admission Procedures
Recruitment of first-year students directly into the BIT Program through the MCSB Gateway will be performed in a manner similar to recruitment of first-year students into other campus graduate programs.
The Biomedical Informatics Training (BIT) Program. ME, Mol. Evolution track in Ecology and Evolution Dept.; MBGB, Combined Mol. Biol., Genet. and Biochem Program in School of Biol. Sci.; CB, Chemical Biol. Track in Chem Dept.; IBAM, Informatics in Biology and Medicine track in ICS; BME Biomedical Engineering Program. Existing graduate programs and BIT cooperate to jointly admit first year students directly into the MCSB Gateway. Alternatively, second-year students can join the BIT Program at the beginning of their second year as in the past.
Nomination Process
Applications for acceptance into the BIT Program will be received directly from first-year applicants. Applications accepted for admission by the BIT Steering Committee will be secondarily evaluated by the admissions committee of the campus graduate program in which they will receive their Ph.D. degree. Only applicants qualified for both programs can be accepted into the BIT Program. Criteria for acceptance in both programs is based on the student’s undergraduate and graduate academic and research record, GRE scores, and reference letters. Students with superior research experience, academic records, and GRE scores above the 75th percentiles will qualify for acceptance. Upon acceptance into the BIT Program, first-year students will be assigned a BIT faculty advisor in their primary area of interest. At the end of the first year of study, those students who successfully fulfill training program requirements and pass their program qualifying examinations, will select a BIT Program thesis advisor. As soon as possible, no later than the beginning of the winter quarter of the second year, the students together with the consultation of the BIT Program Steering Committee and their thesis advisor will select a cross-discipline co-thesis advisor. In most cases, this will be an investigator with ongoing collaborations with the student’s thesis advisor in areas related to the student’s thesis research.
As in the past, nominations for appointment of second-year graduate students to the BIT Program will be received from a student’s BIT Program faculty thesis advisor in an existing campus graduate program. These applicants will be evaluated by the BIT Program Steering Committee using the same criteria used for the admission of first-year students. In addition, their first year performance in UCI graduate courses and research rotations will be considered. Upon acceptance into the BIT Program, a cross-discipline thesis co-advisor will be assigned to each student. In most cases, this will be an investigator with ongoing collaborations with the student’s thesis advisor in areas related to the student’s thesis research.
Mandatory Courses
By the end of the first quarter of the second year, all students - whether they enter the BIT Program in their first year through the Gateway or in their second year though a BIT-affiliated graduate program - must have satisfactorily completed a high level language programming course equivalent to CS 21. The CS 21 course provides students with an introduction to fundamental concepts related to computer software design and construction, and design and programming skills, primarily using PERL and C++/Java/Python, emphasizing biological data and applications.
By the end of the second year of the BIT Program, all BIT students must pass the following four required BIT Program courses:
CS 284A. Representations & Algorithms for Molecular Biology (4) Winter quarter - Lecture (3 hrs.). Introduction to computational methods in molecular biology. Biological sequence analysis. Computational approaches to understanding and predicting the structure, function, interactions, and evolution of DNA, RNA, proteins, and related molecules and processes.
CS 284B. Probabilistic modeling of Biological Data (4) Spring quarter - Lecture (3 hrs.). A unified Bayesian probabilistic framework for modeling and mining biological data. Applications range from analyses of sequence data (DNA, RNA, proteins), to protein structure prediction, to genome annotation and the interpretation of high-dimensional gene expression data. Applications of statistical machine learning methods, including graphical models, Markov models, stochastic grammars, kernels, and neural networks are emphasized.
CS 284C. Computational Systems Biology (4) Spring quarter - Lecture (3 hrs.). Introduction and development of software tools and packages for the computational inference and non-linear dynamic modeling of metabolic pathways, gene regulation networks, signal transduction pathways, and the functions of these networks in cellular processes, development, and disease.
MMG 250. Responsible Conduct of Research (2) Spring quarter. Every BIT Program student and postdoctoral fellow is required to take the UCI Responsible Conduct of Research course, no later than the end of the third year. This course, MMG 250 (2 credits), is offered each year during the spring term. All students on NIH training grants are required to participate in this course once during their training at UCI. The intent of this course is to introduce students to the complex issues involving scientific integrity, while meeting the requirements for training in bioethics for students supported on NIH training grants. The format for the course is informal and designed to engage students in discussion.
By the end of the third year of the BIT Program, all students must pass the following or equivalent two additional courses:
Eco Evo 207. Quantitative Methods in Biology (4) Winter quarter – Lecture (3 hrs.). Statistics for biologists. Emphasis on specific applications and underlying assumptions rather than on methods of calculation. Topics include experimental design, parametric and nonparametric methods, analysis of variance and covariance, and multiple regression.
CS 122A. File and Database Management (4) Winter & Spring quarter – Lecture (3 hrs.). Database system architecture--data structures, storage structures, and data languages. Alternate approaches to database management systems: relational approach, hierarchical approach, network approach. Database security and integrity. Query processing.
*Course numbers are subject to change. Please refer to the most recent UCI General Catalog.
Most of the BIT-affiliated graduate programs require their students to take one elective course each academic year. The BIT courses described above will fulfill this requirement.
Click here for course requirements for BIT trainees who entered the program before AY06-07.
Laboratory Rotations
In addition to didactic training, laboratory rotations constitute an important component of the first-year program, providing students with intensive introductions to experimental design and quantitative data analysis, as well as introducing them to available research opportunities. Each quarter, each BIT Program student will conduct a rotation in the laboratory of a BIT faculty member, prior to choosing a primary thesis advisor at the end of the first year. Because of the interdisciplinary nature of the BIT Program and the diversity of the participating students, it is important that students become familiar with both “wet” experimental biology labs as well as with computational labs. Therefore, students entering the program with a computational background are required to do one rotation in a biology laboratory and students with a biology background are required to do one rotation in a computational environment. Students are encouraged to pair up for interdisciplinary, collaborative work during their rotation experiences.
Choosing a BIT Faculty Thesis Advisor
Throughout the first two quarters of each year, BIT faculty will present informal “Pizza Seminars” describing their research interests to the BIT Program students. These presentations are a key mechanism by which students become familiar with various potential research areas prior to choosing research laboratory rotations and a thesis advisor. All first-year BIT Program students are required to attend these seminars and to select a primary thesis advisor at the end of the first year.
Continuing BIT Program Requirements.
IGB and Home Department Seminars. All BIT students are required to attend seminars sponsored both by their home department and by the IGB. The IGB seminars most often emphasize computational aspects of biomedical informatics and computational biology. The home department seminars emphasize topics in the student’s primary area(s) of expertise.
BIT Lunch. Trainees meet as a group the first Monday of each month for lunch. At these lunches the trainees are free to openly discuss their research projects and develop closer professional and personal ties with one another. The BIT lunch is facilitated by a BIT group Web site hosted by the trainees. At a typical BIT lunch, a biology trainee(s) might informally present their ongoing research, highlighting areas where they need bioinformatics assistance or input from computer scientists and/or computational biologists. At that point, the computation students might offer advice and explain the basis of computational methods and/or algorithms to address the problem. Often, appropriate algorithms or computational methods must be devised to deal with the problem. Sometimes the solutions are trivial, but at other times they develop into collaborations among the members of the group. Occasionally, the student’s invite BIT faculty or visiting scientists from other academic institutions or industry to discuss their interests with the group as well as host career development sessions.
Student Research Presentations. Each month, two program students are required to present a formal seminar to the training grant faculty and their research groups. This provides the students with the skills necessary for communicating their work to an interdisciplinary scientific audience. Every student in the program is required to present at least one seminar each year.
Annual Trainee Mini-Symposium. Each year in the spring, the Institute for Genomics and Bioinformatics sponsors an all day symposium for the trainees to present their research results. This has proven to be a very successful event. The students work very hard on their presentations. Each year this event has been very well attended by UCI faculty and student researchers from many disciplines across the UCI campus. Click here for the 2008 BIT Symposium program and abstracts.
Attendance and Participation in National Meetings. All students are encouraged to attend national meetings to broaden their perspectives of current topics and methods in biomedical informatics and computational biology research. Training grant and IGB travel support for those students presenting their research results at a national meeting is given top priority. Each year the BIT Program Trainees present their research at the NIH-NLM Directors meetings held in Bethesda or on the campus of another NLM training grant awardee.
