MS Bioinformatics, Bioinformatics Graduate Program

Key Steps

  • Enroll in CS 200W (if necessary)
  • Find an advisor
  • Understand the rules about plagiarism
  • Enroll in CS 297
  • Submit application for candidacy.
  • Form a committee
  • Submit CS 298 (or 299) proposal and graduation form.
  • Enroll in CS 298 (or 299)
  • File application for award of degree
  • Defend your writing project/thesis
  • Submit your report for publication

The Competency in Written English Requirement

  • You must satisfy the Competency in Written English requirement. For most students this means taking CS 200W. This is a co-requisite for CS 297 and a prerequisite for CS298/299.
  • The University requires that all graduate students complete the Graduation Writing Assessment Requirement (GWAR) as a condition for advancement to candidacy. The Computer Science Department policy is that students should complete the GWAR requirement (usually by taking CS200W) in their first year in the MS program and must complete it two semesters before graduation.
  • You must have satisfied the Competency in Written English, or you must be enrolled in an approved technical writing course in order to enroll in CS 297.
  • You must have satisfied the Competency in Written English requirement to enroll in CS298/299. No exceptions!

Preparing for the Project

  • MSBI students are required to complete a 2-semester thesis (297 + 299, also called "Plan A" in the university catalog) or writing project (297 + 298, also called "Plan B").
  • If you choose the thesis or writing project path, you must decide whether you want to work on a writing project or a thesis. The principal difference is that the writing project will not be filed with the Associate Vice President of Graduate Studies and Research. The Graduate Studies office is very stringent about English language usage and typography of theses.
  • You must find an advisor who is willing to work with you. It is a good idea to be flexible and be prepared to work with one of several potential advisors.
    You and your advisor must agree on a topic for your project. Again, it is a good idea to be flexible and find a topic that is of interest to you and your advisor.
  • You should start contacting potential advisors by the middle of the semester preceding the start of the project.
  • Projects must have appropriate depth for graduate work. "Literature review" and "routine implementation" projects will not be approved by the department. Projects that are merely lengthy but shallow are not appropriate. In particular, you need to be able to demonstrate how your project rises above the level of a senior undergraduate project. We consider the following criteria:
    • technical innovation: are you using new techniques that have not been used in this way in the past?
    • technical challenge: are the tools and techniques that you are using so difficult that they require the maturity of a graduate student?
    • theoretical foundations: are you providing a theoretical framework for your work, for example by discussing architectural patterns, by analyzing the relationships between your implementation and prior art, or by performing a mathematical analysis?
    • quantitative analysis: are you gathering and evaluating quantitative data?
    • Your project deliverables should show that your project meets one or more of these criteria.
  • The results of your project (i.e. the final report and the source code) must be available for public inspection. Proprietary work is not appropriate.
  • Be sure that you understand the plagiarism policy.


  • Present a proposal (1-2 pages) to your project advisor that includes
    • a description of your project
    • a proposed schedule for your project work
    • a tentative list of proposed deliverables
    • a list of literature references
  • If your advisor approves, you will receive an add code for CS297.
  • Remember to file your candidacy form as soon as you have started with your CS297 class. See the Graduate Studies page for candidacy deadlines. If you don't file this form by the deadline, you won't be able to progress to CS298.
  • Complete the candidacy form if you are:

    1. Fully classified
    2. Completed CS 200W
    3. Enrolled in CS 297

    View the  MSBI Guidelines for Completing the Candidacy Form [pdf] [pdf]

    Please email the completed candidacy form and unofficial transcripts to Jutomue Quenavah (

  • It is strongly suggested that you do some implementation work and some writing in the first semester.
  • At the end of the first semester, you report your progress to your advisor and your committee members. Your advisor determines how this should be done (a report, a presentation to the committee, etc.)

The Committee

  • You and your advisor need to find two additional committee members to form a 3-member project committee.
  • The advisor and at least one other committee member must be a permanent member of the CS faculty.
  • You must form the committee by the end of the first semester.
  • If at any time you need to change the committee, you need to have written approval from the department.
  • You need to keep your committee members updated throughout your project.
  • Meet with them at least three times (at the end of the first semester, a month into the second semester, and when you are about to complete your work).
  • Solicit their input early so that you are not surprised by requests for enhancements late in the project or even worse, the defense.
  • In the defense, all committee members must agree that your work is complete and correct. Committee members have the right and the obligation to reject substandard projects. 

The 298/299 Proposal

  • To continue your project, you need to file a 298/299 proposal (1-2 pages) with the department. In the proposal, you need to list your, your advisor's and committee members' names, email addresses, and affiliations (if not SJSU CS regular faculty)
    • a description of your project
    • a summary of your 297 results
    • a proposed schedule for the completion of your project
    • a concrete description of deliverables in your software and report
    • a description of the challenging and/or innovative aspects of your proposal
    • a list of literature references

If you are retaking CS 298/299 and your proposal has not changed, add a statement: "This is a continuation of the CS 298/299 project that was approved for (insert semester), and there are no changes to the proposal."

  • Your proposal must be in proper English. The department may reject plans that contain too many spelling or grammar errors.
  • File your proposal within one week after the first day of classes of the semester in which you want to to take 298/299. (You may file it at the end of the preceding semester if you prefer.)
  • As a rule, instructors and the department are unlikely to agree to the supervision of projects over the summer, due to travel plans and reduced compensation for summer classes. If you want to take the course over the summer, and your instructor and the department chair agree to it, you must file the form no later than two weeks before the last day of classes of the preceding Spring semester.
  • File the CS 298 request form and your graduation form [pdf] at the department office with a printout of the 298/299 proposal. We ask that you submit your graduation form with your 298/299 application so you don't forget to file it. See the Graduate Studies page for graduation form deadlines.
  • Upon approval, you will receive a registration code from the department.

The Second Semester (298/299)

  • Complete your experimental or implementation work early enough to give you ample time to finish your written report. Here is the LaTeX template for the 298 report. 
  • Give your committee members at least a month before your defense date to read and comment on your written report.
  • Your report should be about 40 single-spaced pages. That said, you can choosee to write the report in either single or double-space.
  • Follow the Graduate Studies formatting instructions
  • Your report must be in proper English. It is your job--and not that of your advisor or committee members--to proofread your report and fix any spelling and grammar errors before you give it to your committee to read. Your advisor and committee members are responsible for reviewing the technical contents of your report, not your spelling and grammar.
  • Your committee--or in the case of a thesis, the Graduate School--has the right to reject your report if it is not written in proper English.
  • You must submit the draft report at least two weeks before the scheduled defense. Please email  to be added to the "Plagiarism Check of MSBI 298/299" course on Canvas. Once you are added to the course, please submit your report under "assignments." Next you will need to fill out, and submit an Oral Defense Room Request Form [pdf]. Please submit this form to .
  • Contact the office to request a room assignment. You will receive it after the plagiarism check has passed. The office will post an official announcement of your defense.
  • The defense date must be before the last day of the semester. It is strongly suggested to schedule the defense before the first day of finals.
  • If you schedule your defense during finals, it may happen that no room is available. It is acceptable for you to reserve a room in Clark Hall or the library.
  • Any rescheduling of the defense requires two weeks notice.
  • If you do not follow this procedure (that is, if you simply find your own room and hold the "defense" there without plagiarism check and an official announcement), you will not be allowed to graduate.

The Defense

  • The defense must have been officially announced by the department in order to be valid.
  • The defense is open to the public.
  • You need to procure any necessary projection equipment.
  • In the defense, you will give a presentation of your project and answer questions from the committee and the audience. You should bring a printed copy of your written report to the defense and make it available to the audience.
  • The committee may request modifications to your work.
  • You need to get your advisor's and your committee members' signature which the department office should have prepared for your advisor.
  • Turn in that form to the department office.
  • Defense must be completed before/on the last day of final exams.


Your Final Report

  • Produce a PDF file with name lastname_firstname.pdf where firstname,lastname are your first and last name in lowercase. For example, John Q. Nguyen would send a file nguyen_john.pdf, that is, the six lowercase letters n g u y e n followed by an underscore (U+005F), the four lowercase letters j o h n, a period (U+002E), and the three lowercase letters p d f. Do not zip the file.
  • The cover page of your report should contain your name and the title of your project in Title Case (not all uppercase) and the publication year. You must supply an abstract (a single paragraph, < 1000 characters). Your abstract must be legible on its own. Do not include page references, section references, or literature references. Your abstract must consist of UTF-8 characters that can be copied out of Adobe Acrobat. If you use TeX, you must figure out how not to have ligatures appear as invalid characters. 
  • Include up to 6 keywords below the abstract (on the same page).
  • Once you made any final changes to your report, ask your advisor to send it to the MS Bioinformatics Program Coordinator:
  • The report will be posted on (by default) or, for the first year on a protected web site (by your or your advisor's written request, to allow for publication)
  • Once you have seen your report published, you can ask the MSBI program coordinator to send a "Culminating Experience Memo" to Graduate Studies. That will trigger your graduation.