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GENERAL EXPECTATIONS FOR CBM GRADUATE STUDENTSACADEMIC STANDING AND EVALUATION OF STUDENT PROGRESS– Students areexpected to maintain good academic standing during the course of their participationin the CBM program. Academic standing will be determined by the policies andprocedures of the graduate school in which the student is matriculated. It is expectedthat CBM students will, at a minimum:o Achieve grades of B or better in all coursework;o Successfully complete all laboratory rotations;o Successfully complete either the Admission to Candidacy Examination (“A”or “ACE” Exam) the Qualifying Examination (Q Exam), or the ThesisProposal Examination (TP Exam) (the type of examination to be taken isdependent on the institution at which the student chooses to pursue his/herthesis research);o Demonstrate adequate progress in thesis research project;o Successfully complete a thesis defense and submit a written thesis inaccordance with the policies and procedures of the graduate school in whichthe student is matriculated.Students are also expected to abide by any other policies and procedures of thegraduate school in which they are matriculated and to participate in any requiredjournal clubs and/or other activities required by the CBM Program administration.Failure to maintain good academic standing may lead to the student being placed onacademic probation or being dismissed from the graduate program. Placing a studenton academic probation and/or dismissing a student from the program will begoverned by the policies and procedures of the graduate school in which the student ismatriculated and will be done in consultation and with the approval of the CBMProgram Director.LABORATORY RESEARCH ROTATION ADVISORS - The research advisors submitwritten reports on the student’s performance during each of the research rotations.The reports are forwarded to the Tri-Institutional Program Office, which will send acopy of all evaluations to the Graduate School in which the student matriculates. (Theevaluation form is reproduced in the Appendix). Each student is also expected tosubmit an evaluation of his/her experience in the laboratory rotation. These reportswill be submitted to the Tri-Institutional Program Office and will be keptconfidential.T HESIS DEFENSE COMMITTEE - Following the thesis defense examination, thethesis defense committee (which consists of the Thesis Advisory Committee plusexternal examiners) will submit a written report on the results of the examination.The report is forwarded to the Tri-Institutional Program Office, which will send acopy of the report to the Graduate School in which the student is matriculated.D URATION OF TRAINING – It is expected that students will complete their thesisresearch and graduate degree within six years of matriculating into the graduateprogram.7

CBM TIMETABLE OF ADMISSIONS AND TRAININGADMISSIONSDeadlineJanuary 1Early - MidFebruaryMid FebruaryMarchApril 15DescriptionResponsible PartyApplication deadline.StudentApplicants invited to interview in NYC (Phoneinterviews conducted when necessary)CBM Program DirectorSelected applicants visit NYC for open house andinterviews, after which CBM program makesadmission decisions for applicantsCBM Program DirectorAcceptance letters mailed outCBM Program DirectorStudents accept offers of admission to programStudentPRE-MATRICULATIONDeadlineMay 1June 15DescriptionI-20 visa applications completed and submitted toGraduate Admissions Office at CU-I (foreign studentsonly)Responsible PartyStudent to complete the application forsubmission, CU-I Graduate Admissionsto process I-20Students notified of summer housingCBM administrationSUMMER SESSION, YEAR-01 (NYC)DeadlineFirst work day afterJuly 4DescriptionStudents begin summer program in NYC, featuring 6week laboratory rotations, faculty researchpresentations, and student journal club.Responsible PartyCBM Program DirectorFIRST SEMESTER, YEAR-01 (ITHACA)DeadlineOrientation WeekDescriptionEach student is assigned a temporary major advisor from theCornell University pool of Computational Biology GraduateFieldSeptember DecemberStudents take graduate level courses according to theAcademic Requirments of the Computational Biology Fieldat Cornell University.Responsible PartyIthaca Computational BiologyGraduate Field administratorStudentWINTER INTERSESSION YEAR-01 (NYC)DeadlineDecember 1December 1First week inJanuaryDescriptionStudent must make arrangements for and notify CBMAdministration of choice of labs for NYC January sessionmini-rotationsStudents notified of January session housingStudents commence in NYC and spend intersession pursuingmini lab rotations and daily journal clubsResponsible PartyStudentCBM administrationCBM Program Director8

CBM TIMETABLE OF ADMISSIONS AND TRAINING (CONTINUED)SECOND SEMESTER YEAR-01 (ITHACA)DeadlineMid JanuaryFebruary 1DescriptionCBM students return to Ithaca to continue approvedgraduate level courseworkHousing arrangements must be made for Year-2 SummerSession in NYCResponsible PartyStudentCBM administrationSUMMER YEAR-02DeadlineMayJuly 1DescriptionStudents begin summer session in NYC including:o Lab rotationso Research Lunch Talks/Journal ClubsDeadline for selection of thesis lab (and therefore whetherstudents will return to Ithaca or stay in NYC).Responsible PartyCBM Program DirectorStudentYEAR-02 and BeyondDeadlineAugustDescriptionStudents who have chosen WMC or SKI labs remain inNYCAugustStudents who have chosen Cornell University labs return toIthacaTBAStudents who have chosen NYC labs must complete andsubmit an Application for Change of Enrollment to anotherCampus form to the CU-I Graduate School OfficeFall Semester, Yr 2 A or Ace Exam: All students will write and defend a thesisproposal for their A exam or ACE exam. The exam must besuccessfully completed and registered according to theguidelines of the graduate school in which the student ismatriculated. Originals of all required forms must be filedwith the appropriate graduate school, and duplicates mustbe filed with the CBM office.AnnuallyAnnual meetings of the Thesis Advisory Committee must beheld and a report filed with the CBM administration and theappropriate graduate school office.Responsible PartyStudentStudentStudents must submit form toCU-I CBM administrationStudentStudentAT ALL TIMES IN THE CBM PROGRAMDescriptionStudents are required to abide by all of the policies and proceduresof the graduate school in which they are matriculated for their thesisresearchALL CBM students are required to participate in:o CBM journal clubs and seminar serieso Annual Tri-Institutional CBM symposium/retreat(CU-I students participate in existing journal clubs and researchpresentation forums on the Ithaca campus)Responsible PartyStudentThe student is responsible formeeting ALL deadlines. Failureto comply with any deadlinemay result in the student’s statusbeing placed on hold, thuspreventing them from registeringfor future semesters. The CBMprogram staff will facilitate thecoordination of these processes.9

CBM ADMINISTRATION AND CONTACT INFORMATIONDIRECTORS:Program Director:David J. Christini, Ph. D.Dept. of MedicineWeill Medical College, Starr 463520 E. 70th St .New York, NY 10021(212) 746-6280dchristi@med.cornell.eduKathleen E. PickeringExec. Director Tri-Institutional ProgramWeill Medical College, Room Olin Hall 201445 East 69th Street, New York, NY 10021(212) her MoranProgram AdministratorWeill Medical CollegeDept. of Biochemistry, W-2011300 York Ave New York, NY 10021(212) 746-5267 hem2008@med.cornell.eduBecky StewartAssistant Director of Computer Science Grad Program4126 Upson HallCornell University Ithaca, NY 14853(607) 255-8593bstewart@cs.cornell.eduHOUSING CONTACTSWeill Medical College Housing Office:Andrew Kaneakjane@med.cornell.eduMichael Sacksmis2025@med.cornell.eduAsa Folukeakf2001@med.cornell.edu420 E. 70th St. Room 2S(212) 746 – 1001; (212) 746 – 1016Helmsley Medical Tower1320 York Avenue @ 70th St.(212) 472-8400Cornell University Housing Office, Ithaca:Office of Campus Life205 Robert Purcell Community CenterIthaca, NY 14853-6001(607) 255-5368GRADUATE SCHOOL/GRADUATE FIELD OFFICESWeill Medical College Graduate SchoolFrançoise Freyreffreyre@med.cornell.eduNoreen Smithnvsmith@med.cornell.eduDenise Jenkinsdjenkins@med.cornell.edu445 E. 69th St. Rm 412(212) 746 - 6565Cornell UniversityGraduate Field of Computer Science Office4130 Upson HallIthaca, NY 14853-7501Telephone (607) 255-731610

HOUSINGDuring the first summer of the program and the first winter intersession, students will beaccommodated in off-campus housing. At other times, students will be accommodated inone of the participating institution’s housing. Where possible, students choosing NYCmentors will be accommodated in housing units of the graduate school in which thestudent is conducting his/her thesis research.GUIDELINES GOVERNING SCIENTIFIC MISCONDUCTINTRODUCTION AND DEFINITION.Truth, integrity and credibility are critical anddistinctive principles of any educational/research institution. Adherence to theseprinciples is essential for the efficient progress of scientific research and to preserve thetrust of the public in the research community. The maintenance of accepted standards inresearch based on these principles is highly regarded by the scientific community and is amajor responsibility of CU-I, WMC, and MSKCC. Consequently these institutions mustset standards and procedures for their members in order to preserve the truth, integrityand credibility in research to prevent scientific misconduct, and to deal efficiently andfairly with allegations or other indications of scientific misconduct.Scientific misconduct is generally defined as an act that violates the standards of integrityin the conduct of scholarly research or communication. Such acts include, but are notlimited to:o Plagiarism – the representation of words or ideas of others as one’s own; moresubtle practices include misleading or inadequate reference citation and duplicatepublication of identical data without adequate reference;o Falsification of Data – direct fabrication of results, misrepresentation of methods,or deliberate omission of conflicting data with intent to deceive;o Forgery of Scientific Documents;o Abuse of confidentiality – misuse of confidential information or failure tomaintain the confidentiality of such information, e.g., “stealing” of informationobtained through review of research proposals, manuscripts, etc.;o Aiding or facilitating acts of academic dishonesty by others;o Violation of pertinent Federal or institutional regulations and ethical codes, e.g.,those involving protection of human subjects and the welfare of laboratoryanimals;o Other practices that seriously deviate from those that are commonly accepted inthe scientific community for proposing, conducting or reporting research;o Breaches of scientific integrity other than those enumerated above;Honest error or honest differences in interpretation or judgment of data are not regardedas scientific misconduct.11

GUIDING PRINCIPLES FOR PRESERVING RESEARCH INTEGRITY - The administration,faculty, students and other academic or non-academic staff all share in the responsibilityfor preserving research integrity and preventing scientific misconduct. This policyapplies for all such individuals associated with the Tri-Institutional Training Programsand within the participating institutions. Together they must create an atmosphere thatpromotes high ethical standards and fosters honest research. Within this framework, it isthe institutions’ obligation to establish standards and responsibilities for their membersand to hold those members accountable for transgression of these regulations.Accordingly, the institutions consider violation of the tenets described above under“Introduction and Definitions” to represent a major breach of contract between thefaculty, student or staff member and the institutions.RESPONSIBILITIES OF FACULTY, STUDENTS AND STAFFo Faculty, students and staff through appropriate and timely openness ofresearch should foster intellectual honesty. Upholding intellectual honesty isthe responsibility of all institutional members, especially the scientific leadersand laboratory directors and faculty. These individuals must set the exampleby maintaining the highest ethical standards, encouraging opencommunication within and amongst laboratories and laboratory workers, andinstituting procedures for self-regulation and peer review of ongoing research.Faculty, students and staff are urged to discuss research ethics to heightenawareness and recognition of these issues.o Faculty, laboratory directors and scientific leaders must accept specialresponsibility for the appropriate supervision and teaching of other staff andstudents, and in the final analysis, must assume responsibility for the validityof all research communications emanating from their laboratories.o Carefully recorded experimental protocols and methods are strong deterrentsto research misconduct. It is the responsibility of the researcher to ensure thatrecords are maintained to document adequately the work performed.o Faculty, staff and students should insist on the appropriate accreditation ofauthorship for their own work and should cite appropriate references toresearch performed outside their laboratories. The contributions of otherinvestigators should be appropriately acknowledged in all scientificpublications. Authorship should be attributed only to those individuals whohave contributed significantly to the research, have reviewed the manuscriptcritically and who are prepared to support the validity of the data presented.o The faculty, students and staff, as members of the scientific communityshould report any incident of scientific misconduct which they believe to haveoccurred, or any allegations of scientific misconduct which are brought totheir attention.PRODECURES - Any allegations of scientific misconduct pertaining to a student will bemanaged in accordance with the policies and procedures of the institution at which thestudent is matriculated. Allegation(s) of scientific misconduct pertaining to a staff orfaculty member will be managed in accordance with the policies and procedures of theemploying institution. Students and faculty of the Tri-Institutional Training Programs areexpected to familiarize themselves with the appropriate institution’s policies andprocedures governing scientific misconduct.12

APPENDIX13

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TRAINING PROGRAM IN COMPUTATIONAL BIOLOGY & MEDICINECourse selection approval formStudent se return this form to the TIRP Program Assistant, Heather Moran, by Emailhem2008@med.cornell.edu or Fax: 212-746-484315

TRI-INSTITUTIONAL RESEARCH PROGRAMTraining Program in Computational Biology & MedicineFACULTY EVALUATION OF STUDENT PERFORMANCEA CBM student worked in your laboratory as a rotation student in partial fulfillment ofthe requirements of the CBM Program. We would appreciate it if you would evaluatethis student’s performance.The evaluations are filed in the CBM Office.Student’s NameYear in ProgramFaculty Rotation AdvisorSummer (add year)SatisfactoryUnsatisfactoryLaboratory skillsKnowledge of rationalefor experimentsAbility to applyknowledgeAbility to reasonAbility to tionCreativityRelationships withlaboratory personnelPotential for career inbiomedical researchOverall evaluation16

Brief description of rotation projectDetailed comments regarding student’s performanceSigned (print name in lieu of signature for electronic filing)DatePlease return to the CBM Program Assistant by Email hem2008@med.cornell.eduor Fax: 212-746-484317

TRAINING PROGRAM IN COMPUTATIONAL BIOLOGY & MEDICINESTUDENT EVALUATION OF ROTATIONAs a CBM student, you worked in a laboratory as a rotation student in partial fulfillmentof the requirements of the CBM Program. We would like to know your opinion.The evaluations are filed in the CBM Office and are confidential.Student’s NameYear in ProgramFaculty Rotation AdvisorDates of RotationLaboratory Research TopicPlease check one:YesSomewhatNoWere you well received in thelab?Did you feel involved in theresearch?Did you gain laboratory skills?Did you gain knowledge in theresearch topic?Was your ability to applyknowledge and reasonincreased?Were you given opportunityfor independent work?Did your interest level in theresearch topic increase?Did your interest in a career inbiomedical research increase?Was your overall experiencepositive?Would you consider thisadvisor as a potential mentor?18

Brief description of rotation projectAdditional comments/suggestionsSigned (print name in lieu of signature for electronic filing)DatePlease return to the CBM Program Assistant by Email hem2008@med.cornell.eduor Fax: 212-746-484319

TRAINING PROGRAM IN COMPUTATIONAL BIOLOGY & MEDICINESTUDENT-FACULTY LAB ROTATION AGREEMENTLab Rotations are an important part of the CBM graduate training program, andare designed to help students select a faculty laboratory for their thesis research.The rotations are, of course, a “two way street”, allowing the student to becomefamiliar with ongoing research activities and personnel in individual labs, and thefaculty member to assess the interests and skills of each student. In order to achievea harmonious match, student and faculty member should meet prior to the start ofthe rotation to discuss their goals and expectations, and then formalize thediscussion by completing the signing of this form.Student Name:Year in Program:Faculty Rotation Advisor:Institution:Rotation Start Date:Rotation End Date:1. Briefly describe the general area in which the student will participate:2. List the name and title of personnel who will provide direct student supervision:3. Please agree on an anticipated schedule of hours and complete the table providedbelow:DaySunMonTuesWedThursFriSatHours4. Briefly describe specific student activities for the rotation:a.Lab work:b.Readings (feel free to attach a list of references) and writing (paper, proposals,etc.):c.Participation in lab meetings or other presentations:20

5. Briefly describe the anticipated goals for the rotationBrief description of rotation projectAdditional comments/suggestionsFaculty SignatureDateStudent SignatureDatePlease return this form to the TIRP Program Assistant, Heather Moran, by Emailhem2008@med.cornell.edu or Fax: 212-746-4843.21

CBM FACULTY ROSTERMSKCCWMCCU-IGrégoire Altan-BonnetColin BeggEric LaiAlex LashChris SanderJaya SatagopanJose VilarOlaf AndersenEmre AksayDouglas BallonAdele BoskeyFabien CampagneDavid ChristiniColleen ClancyDavid EliezerDaniel GardnerDiana MurrayJonathan VictorHarel WeinsteinTimothy WrightCarlos BustamanteAndrew ClarkRon ElberRobert GilmourJohn GuckenheimerUri KeichKelvin LeeChristiane LinsterHod LipsonJason MezeyRichard RandSteve SchwagerJim SethnaDavid ShallowayAdam SiepelEric SiggiaSteve StrogatzMarjolein van derMeulen22

Cornell University Memorial and Sloan-Kettering . Executive Director Program Administrator Tel: (212) 746-6049 Tel: (212) 746-5267 kap2013@med.cornell.edu hem2008@med.cornell.edu GRADUATE FIELD OF COMPUTATIONAL BIOLOGY . education throughout the graduate training.