BEE Graduate Student Handbook

Overview & Introduction

The Biological and Environmental Engineering Graduate Student Handbook is prepared to assist both new and continuing graduate students, not only with their studies, but also with policies and procedures of the Department of Biological and Environmental Engineering (BEE) as well as general policies of the Graduate School at Cornell University.

These guidelines should be used as a guide to the specific activities within the Field of Biological and Environmental Engineering and the Department of Biological and Environmental Engineering. Additional valuable information is available in the Guide to Graduate Study sent to all new graduate students and available at the Graduate School in Caldwell Hall. The Cornell University Courses of Study catalog is also a useful tool and is available through the Graduate School.

Overall administrative responsibility for the Biological and Environmental Engineering Graduate Field rests with the Graduate Coordinating Committee chaired by Professor Sunny Jung.

Questions for this committee should be directed to Professor Jung, Director of Graduate Studies (DGS) for the Field.  Questions about the graduate program should be directed to either Professor Jung, or to Brenda Marchewka, Graduate Field Assistant (GFA), bee-grad [at] (bee-grad[at]cornell[dot]edu).

For purposes of administration, the Director of Graduate Studies automatically becomes your Committee Chairperson if you do not submit this change in Student Center within the first three weeks of your first semester of graduate study. The remainder of your Special Committee should be in place by the end of your second semester of study for MS and third semester of study for PhD. MS and MPS require a committee of two graduate faculty.  PhD requires a committee of three graduate faculty. MEng requires a project supervisor who is a graduate faculty member in BEE.

Please become familiar with the information available to you concerning graduation requirements. The Graduate School places the responsibility on you to know and meet all requirements.

Important information for graduate students

University Policies

Detailed information on Graduate School policies is available from the Graduate School located in Caldwell Hall.

A graduate student in residence in Ithaca must be registered and pay tuition for that part of the term while on campus, even if engaged in thesis writing and taking no courses.

Students must register during the summer if they are 1) receiving financial aid during the summer (such as summer loans, assistantships and fellowships, travel grants, or tuition awards); 2) wish to use campus facilities during the summer; or 3) are off campus but need to be registered for summer study.  Graduate students who have been registered for a regular semester during the preceding academic year do not pay tuition for noncredit summer registration.  Students approved for summer residence credit must pay the appropriate prorated Graduate School tuition rate.

Graduate Degree Programs
Four different degrees are awarded in the Graduate Field of Biological and Environmental Engineering: Doctor of Philosophy (PhD), Master of Science (MS), Master of Professional Study (MPS) and Master of Engineering (MEng).  Detailed academic requirements for each degree can be found in the Guide to Graduate Study booklet, which is published by the Graduate School. 

Special Committees
You will need to nominate the Chair of your committee within the first 3 weeks of registration.  Tuition charges are based on the college that employs the Committee Chairperson.

Degree Requirements and Thesis

Registered Semesters
One registered semester is equivalent to one academic semester of full-time graduate study completed satisfactorily.  Less than satisfactory progress or less than full-time commitment to graduate study could result in reduction of credit to a fraction of a registered semester, or in an extreme case, no registered credit. 

To earn an MS degree, a student must accrue a minimum of two registered semesters and produce and defend an acceptable thesis.  To earn a PhD degree, a student must accrue a minimum of six registered semesters and produce and defend an acceptable thesis.  Two of these registered semesters must be earned between the “A” exam and the “B” exam.

Scheduling of Exams
When scheduling an exam, the first step is to discuss potential dates with your committee chair and minor members.  All necessary forms to complete the scheduling process are available online.  All forms must be completed seven days prior to taking the exam.  Please notify bee-grad [at] (Brenda) of the title of your thesis presentation so that she can announce it to the graduate faculty.  Faculty MUST have seven days notice prior to an exam.  Rooms in Riley-Robb that are available for exams are 205 and 235, Brenda can help you reserve a room.

Thesis Schedule
According to the Code of Legislation of the graduate Faculty, the final examination for the PhD or the defense of the Master’s thesis should be scheduled only when the Special Committee and you are confident that the thesis is virtually in final format but not yet bound.

Two unbound copies of a doctoral dissertation, or two bound copies of a master’s thesis, must be submitted to the Thesis Advisor within sixty days of the exam.  Any changes required by the Committee must be incorporated into the thesis before submitting it to the Graduate School.

If the thesis is not submitted within 60 days, PhD candidates will be assessed a late penalty of $100 in addition to the $200 Active File Fee they must pay for each semester they are not registered in the Graduate School.  If unusual or unavoidable problems with the thesis cause delay in submission, you may petition to have the penalty waived.  The petition must be endorsed by your Special Committee and final approval rests with the Graduate School.

Thesis Publication
If the results of your thesis are to be published, prepare all publications and manuscripts as soon after your final exam as possible.

Advisor - Advisee Relationships
Faculty members develop a graduate education style and student-faculty relationship that they deem appropriate.  Occasionally conflicts occur between a student and a faculty member, whether he or she is a committee member or not.  It is hoped that these conflicts can be resolved by the student’s Special Committee.  If the committee is unable to resolve the conflict, the student should contact the Director of Graduate Studies (DGS), Professor Sunny Jung.  The DGS will discuss the problem with the student and assist in deciding the appropriate action or further referral.  For example, the DGS may call a meeting of the Special Committee or refer the matter to the Department’s Graduate Coordinating Committee.  If the conflict cannot be resolved at the Graduate Committee level, the student may appeal to the Dean of the Graduate School, Dean of the Faculty, or University Ombudsman.

To minimize the possibility of delaying your graduation, you are urged to develop, in consultation with your major Committee Member, a realistic proposal and timetable for your work.

Change of Status
Notify the Graduate Field Assistant, bee-grad [at] (Brenda Marchewka), of your plans for expected date of completion of your degree, leaves of absences, extended absences from campus, and other similar types of activities.  Also, please leave your forwarding address, remove your materials and books from your desk area, return your department keys, and notify the Graduate School of your plans.  In the event of an emergency leave situation, the Student Services Office and/or the Director of Graduate Studies will assist in completing the necessary forms, forwarding of mail, and the like.

Your First Semester of Courses
Many students find themselves at a loss when selecting courses for their first semester.  An interesting option at Cornell is that Grad students are not required to register for courses until a few weeks into the semester.  This freedom allows you to attend courses initially and then choose the best ones.  Your advisor should be able to help you select appropriate courses.  Check with other grads working in your area of interest as well.

The A-exam

To qualify as a PhD candidate graduate students must pass the Admission to Candidacy, or “A Exam”. This exam is used to assess that the student has acquired the necessary tools and is prepared to obtain their PhD.

Candidates must take their A-exam before beginning their seventh semester of graduate school—unless special permission is obtained from the dean. A registration hold will be placed on student’s record for failure to take the A-exam within this time frame. Students must schedule the exam with the Graduate School at least seven calendar days in advance by filing the proper examination scheduling form. Scheduling forms can be found on the Forms pages. All members of the special committee are expected to participate in the examination and evaluate the candidate.

Doctoral students may make changes to their special committee at any time prior to the A exam. Committee changes after an A exam require the dean’s approval.

Format of Exam

The A-exam consists of a written portion and an oral portion. The written portion consists of a thesis proposal which generally outlines the purpose of the proposed PhD research, the questions or hypothesis to be investigated, the methodology used to evaluate the questions or hypothesis and the expertise the student has acquired to perform this research.  The students committee will specify the necessary form and content of the research proposal. The written portion must circulated to the student’s committee at least 2 weeks prior to the exam.

The oral part of the exam is to describe the thesis proposal, the work completed so far, and the students plans for future work. Faculty members outside the committee may be invited to the oral presentation. Following the public presentation is a closed session attended by members of the Special Committee and the graduate student. In this session the committee will ask questions directly or indirectly regarding the student’s proposal. The committee may also ask foundational questions related to the research to ensure that the student has acquired the basic knowledge to complete their PhD. Requirements of the minor will be assessed by minor members of the committee. It is likely committee members will use the time to advice the student as to their research plans.

It is also important the student brings a record of the courses they have taken to date to the exam. Committee members will also assess the courses the student has taken and recommend future courses if appropriate.

Students may be evaluated on the following factors: the problem chosen; demonstration and knowledge in the field necessary to pursue their thesis research; formulation and feasibility of the research methodology; analysis of experimental or numerical data; timeline and feasibility of research; clarity of the research proposal; ability to present and communicate research both orally and in writing; breadth of knowledge.

It is very important that a student discusses the required format of the exam with the special committee well in advance of the exam. In particular, the student needs to ascertain the requirements for their research proposal, any course requirements and any requirements of their minor members prior to the exam. The field recommends the student meet with their special committee annually.


There can be three outcomes of the exam.  1) The student can be given an unqualified pass. For a student to pass an examination, all members of the Special Committee must approve. 2) The student can be granted a conditional pass if weaknesses are found in their exam. In this case the committee specifies the condition(s) and timeline the student must fulfill to pass the exam. Once the special committee confirms these conditions are met the student passes the exam. 3) The student may fail the exam. In this case, if the committee is confident of the student’s ability they may recommend the student retake the exam and will provide them feedback on how to correct any deficiencies. The second exam cannot be scheduled within three months of the failed exam. If the committee assesses finishing a PhD is not in the students best interest they may award the student a masters degree without a thesis or recommend the student complete the program through a master’s degree with a thesis. In either case the student leaves the PhD program. Students passing the exam can be awarded a master’s degree with a thesis.

The committee will communicate the outcome of the examine orally and through a formal written assessment of the student’s strength and weaknesses.

BEE Policies

Right to Know Program
Cornell University has developed a program to comply with the Federal Hazard Communication Standard.  The Biological and Environmental Engineering Laboratory Safety Representative is Lillian Henry.  She is located in 108 Riley-Robb Hall or by calling 607-255-2027.

Lab Orientation Training
All graduate students should plan to attend a training session prior to beginning work in a laboratory or on a farm at Cornell.  Dates (usually at the beginning of each semester), locations, and times are announced a month in advance.

Laboratory Information
Your supervisor is responsible for your orientation and training in the safe handling and use of laboratory specific technologies and chemicals.

Graduate Field
The name of our graduate field is Biological and Environmental Engineering.  The degrees offered are PhD, MS, MPS, and MEng.

Research concentration topics in our Field are the following:

  • Bioenergy and Integrated Energy Systems
  • Bioenvironmental Engineering
  • Biological Engineering
  • Bioprocess Engineering
  • Ecohydrology
  • Environmental Engineering
  • Environmental Management (MPS only)
  • Food Engineering
  • Industrial Biotechnology
  • Nanobiotechnology
  • Sustainable SystemsSynthetic Biology

These topics are used to denote major or minor areas of graduate research.

The MPS and MEng are professional degrees which do not require the declaration of a research concentration.  However, the topics of interest to students pursuing professional degrees closely parallel the research concentrations of the faculty.  The project paper required of both the MPS and MEng typically reflects the special interests of the student.

Application Deadlines for Travel Grants

  • For dissertation research, not conferences
  • Priority is given to PhD students who have passed or will pass the A exam before traveling
  • Awards are 2 times per year: deadline is November 1 for fall/winter, February 1 for spring/summer

Conferral Dates

  • January, May or August


  • Mailed 4-8 weeks after degree conferral date in January, May or August

Exams:  must be scheduled according to the constraints below and in time for project and thesis material to be submitted and accepted by the graduate school and their deadlines.

  • MS: MS Exam, complete all degree requirements, no earlier than one month before completing the minimum semesters of successful registration
  • PhD: A exam, after 2 semesters of successful registration, but before your 7th semester
  • PhD: B exam, complete all degree requirements, 2 semesters of successful registration after passing the A exam

In Absentia

  • November 1 for spring semester
  • June 15 for fall semester

Leave of Absence

  • August 22 for Fall semester; January 15 for Spring semester.After these dates, there may be a percentage of tuition charged and due.
  • Up to 12 months, may be renewed up to 3 times
  • After 4 years, must reapply for admission to the grad school

Registration Deadline

  • Each semester (including summer) unless on a leave of absence
  • You are considered registered with the University once your bill is paid in full and you are enrolled in at least one academic or research course. The deadline for registration to avoid a late registration fee is always by the end of the third week of the semester.

Registered Semesters

  • MS, minimum of 2 semesters of successful registration
  • PhD, minimum of 6 semesters of successful registration; at least 2 after the A exam
  • Non-thesis MS, minimum of 4 semesters of successful registration

Student Progress Review (SPR)

  • Annually after 2nd year, end of Spring semester

Schedule of Examination

  • 7 days prior to exam

Special Committees

  • Chair, first 3 weeks
  • MS, all committee members by the second semester
  • PhD, all committee members by 3rd semester
  • Change special committees 3 months prior to final exam

Thesis or Dissertation

  • Submit complete draft to all members at least 6 weeks before examination
  • At least 5 days before exam, provide all members with complete, typed and editorially acceptable copy for final approval
  • 60 days after passing exam, submit 2 unbound and signed final copies to the grad school
  • After your final exam, you have 60 days to make changes or else will be charged a late filing fee

Time to Degree

  • MS, no more than 4 years between first registration and completion of all requirements
  • Part time, 6 years
  • PhD, 7 years

Financial Aid and/or Assistance

There are two types of assistantships: graduate research assistants (GRA’s) and teaching assistants (TA’s).  TA’s may be assigned to courses taught by faculty who are not involved in the student’s research project.  Administrative details of assistantships are available from BEE Student Services.  However, specific duties or responsibilities will be explained to you by your supervisor.  Tuition for assistants is waived for the fall and spring terms only.  If an assistant registers for summer school or summer research for which tuition and fees are required, the assistant is personally responsible for them.  Graduate students who receive a Cornell paycheck should register during the summer to avoid having FICA and Med Tax deducted.

University Fellowships
Cornell provides the opportunity for graduate students to apply for fellowship programs.  The Fellowship Notebook listing special fellowships administered through the Graduate School can be found on-line at:  You are welcome to review this notebook at any time via the web. 

New York State Tuition Assistance Plan (TAP)
All United States citizens who have been residents of New York State for 12 months prior to the beginning of the semester may be eligible for a TAP award.  The Graduate School or the Bursar’s Office provides application forms as well as answers to any questions you may have regarding these awards.

Income Tax
Representatives from federal and state governments are available during March to answer tax questions.  Contact the Graduate School for specific dates.  Tax forms must be filed and taxes paid by April 15th.

International Services, Office of Global Learning
The Office of Global Learning, located in 300 Caldwell Hall can be reached at 607-255-5243 or on-line at:  The Office of Global Learning offers a variety of information and assistance for international students.

Health Care
All regularly registered students are eligible to use the University’s health facilities.  Cornell Health, located at 10 Central Avenue, is next to Willard Straight Hall.  Cornell Health offers routine office hours during the week, 8:00-5:00 during the school year and 8:00-4:30 during the summer.  They also offer 24-hour telephone triage.  Call 607-255-5155 or if it is an emergency, please contact campus police at 607-255-1111.

All graduate students are mandated to enroll in the Cornell University Student Health Plan (SHP).  Most graduate students will receive SHP coverage as part of their funding packages.  The university will pay the SHP premium for all students who receive full tuition and/or a full stipend from or through Cornell.

The Student Health Plan provides excellent coverage at a reasonable cost. The plan is underwritten by Aetna Life and Administered by The Chickering Group.

Type of Coverage Cost

  • Single Student: $3,792
  • Spouse/Domestic partner: $3,792
  • One child: $3,792
  • Two or More Children: $7,584

Students registered in absentia may still be enrolled in the Student Health Plan, but may be required to pay for the insurance themselves.

There are numerous resources on campus designed to support graduate and professional students. Visit the Graduate School Resources page for a list of common offices and services that many of our students refer to at some point during their graduate career.

Standard Operating Procedures

The mail room is located in 114 Riley-Robb and is open from approximately 8:00 am until 4:30 pm.  Mailboxes are located in the file cabinet near the window. Please check your mailboxes regularly for messages.

Bulletin Board
A bulletin board reserved for graduate study announcements is located in the first floor hallway between Rooms 114 and 116.  The bulletin board is updated regularly by the Student Services Office.

The department fax number is 607-255-4449.  Incoming fax messages are allowed (discretion advised) at no cost to individuals.  Please see your advisor’s Administrative Assistant to send outgoing Cornell-related messages.  No personal faxes may be sent.

If your project director expects that you make frequent purchases, they can request that you gain access to Cornell’s purchasing system, eShop. Permission as well as an account number and detailed business purpose must be obtained from your project or course director before making any purchases. To gain access to eShop, please have your director contact the Financial Reporting Specialist in 112 Riley-Robb Hall. For infrequent purchasers, your director should identify another lab member that can complete your orders.

Department Vehicle
You must have a valid driver’s license and be registered with the Fleet Office at the Fleet Garage before operating any Cornell vehicle.  Check with Lillian Henry in 108 Riley-Robb regarding this procedure.  The department vehicle is to be used for BEE purposes only.  Sign-out sheets are available in Nicole Albright's office in 106 Riley-Robb.

Fleet Garage Vehicles
Similar rules govern the use of fleet vehicles.  A fleet car may be used for official purposes only and charges must be authorized from a departmental account.  Account numbers must be given to the Fleet Garage at the time the vehicle is reserved.  A valid driver’s license must be shown before vehicles are released to drivers.

All vehicles on campus must be registered with the University Transportation Services at 116 Maple Avenue.  Parking on campus is limited and expensive.  Kite Hill parking, just west of Riley-Robb Hall, is popular with BEE affiliates.  Check with the Transportation Services at 607-255-4600 to learn about what other options are available to you.

Additional information

You can find lots of useful information about things happening at and around Cornell, including the weather.  The website is

Student Center
This allows you to be able to check your registration, add/drop classes and make changes to your special committee.

Several labs have computers, so once you are established in a particular lab you will probably have one available at all hours. The lack of computers at off-hours is often an inconvenience to students, new ones in particular. Talk to your advisor if you are having difficulties with computer access.

Several excellent computer centers are available on campus, including ones in Mann Library, Warren Hall, MVR, Upson Hall, and Sibley Hall. Also, Mann Library has a laser printer with lots of fonts.

Using the Research Shop
Blake Werner, Research Shop Manager, is another person to get to know in the department. He is an excellent teacher and has helped many grad students who have little or no experience to construct what they need. 

Small tools, for the most part, can be used with little instruction. Blake requires that you get instruction before using the larger power tools. Safety is of course a primary concern. Blake recommends you “start planning projects early”, by getting in touch with staff members in plenty of time for them to help you. People are helpful but sometimes busy.  Inside the shop there is a scrap box for Plexiglass as well as wood so you can construct a prototype with free material until you find what you want. Tools can also be signed out. The sign out sheet is found next to the shop door.

Dining near Riley-Robb

  • Vet School - great sandwiches
  • Trillium - on-campus dining in Kennedy Hall with a great variety of food and large crowds
  • Big Red Barn - especially for grad students and has pretty good food
  • Stocking Hall
  • More info on Cornell Dining

Campus mail is a free service, provided your mailing is related to University business.  Envelopes (large or small) are available in the mail room and can be mailed in the OUT box for campus mail.

Packages can be sent via UPS or Federal Express with an account number.  You will need to weigh them yourself and fill out the correct forms, which are found in the mail room on the 1st floor.  If you receive a package, you will receive a notice in your box in the mailroom.

LCD Projectors
Computer LCD projectors are available for sign out from the Copy Center.

Cornell Computing
Cornell Information technologies (CIT) is located in the Communications and Computing Center (CCC), 607-255-8990 or helpdesk [at] (helpdesk[at]cornell[dot]edu). They offer a wide variety of computer hardware, operating systems, and general and specialized application programs.  To make these resources readily accessible, CIT operates public computer terminal facilities and provides some free consulting services.

Each student at Cornell is given a unique Network ID consisting of their initials followed by a number.  This Network ID allows students to use electronic mail and several other services in the Bear Access suite.  To have your Network ID set up, you must go to the HelpDesk, first floor, Communications and Computing Center which is located next door to Caldwell Hall.

Computer Crime Legislation in New York
The Associate Dean issued the following information regarding computer crimes.  The New York Senate and Assembly are considering bills that would restructure computer crimes to reflect consequential monetary damages and authorize restitution/reparation.

The Senate and Assembly are also considering Amendments to clarify the definition of “computer virus” and “computer tampering”, to make it easier to convict wrong doers.  Quoting from the Associate Dean, “Beware, the computer crime laws in New York are getting tougher and broader.”

Outdoor Activities Around Ithaca

Here’s a list of some parks and places to see as soon as you can and definitely before you leave Ithaca.  Nothing is all that far and buses run to many of the attractions (277-RIDE).  Take full advantage while you are here!  This is one of the most beautiful places in the US.  If you don’t have an Ithaca map, get one.  You can also get a copy of Trails of Tompkins County by calling 607-275-9487.

  1. Six-Mile Creek, near E. State Street between Cornell and the Commons.  This is a great trail through the forest.  The trail leads to a reservoir and you can go further to Potter’s Falls, which is amazing.
  2. The Wildflower Trail, connected to the area above.  This trail is great for walks by the river and through the forest, especially during the Spring when the wildflowers are all out in bloom.
  3. Upper and Lower Buttermilk Falls State Park, off Route 13.  There are amazing waterfalls and paths.
  4. Treman Park, off of Route 13.  This park is even more amazing.  There is sheer cut rock and natural pools.
  5. Taughannock Falls State park, off of Route 89.  There is a view point overlooking the falls (higher than Niagara) and there are several trails near the falls.
  6. Taughannock Park by the Lake, across from the parking lot of the above.  You can picnic, swim, fish, or watch the sunset, etc.  During the summer there are evening concerts on Saturday’s.
  7. The Plantations, on Cornell campus.  There are beautiful gardens and the grounds extend much further than you can imagine.
  8. Sapsucker Woods, off Route 13.  Cornell Ornithology Labs are there.  This is a nice place for walks through the woods and bird watching.
  9. Shindagin Hollow State Forest, off Route 79 near Caroline.  Great place to mountain bike and ski.
  10. Hammond Hill, off Route 13 East past the airport.  Another great place to walk, mountain bike, and ski.