Doctoral Studies Details

General Information

The Doctoral Study Program (DSP) is accredited at the Faculty of Chemical Technology (FCHT) of the University of Chemistry and Technology, Prague. The DSP Bioinformatics is provided by the Department of Informatics and Chemistry and guaranteed by prof. Daniel Svozil.
The execution of the Ph.D. programme is superivised by the subject-area board (OR). OR monitors and evaluates ongoing studies, approves individual study plans (ISPs) and their changes, proposes the state doctoral exam and PhD defense committees, or approves PhD thesis reviewers. OR meets once a year in January, urgent votes are resolved per-rollam. The OR of DSP Bioinformatics works in this composition.

Study Conditions

The study conditions are described in the Study and Examination Regulations, part VI.

The regular length of the Ph.D. study is 4 years. During this time, the student receives a scholarship and has the opportunity to apply for projects from the Internal Grant Agency (IGA) of UCT. If the thesis is not defended within 4 years, the student can switch to the combined study. Its length is 3 years and during this time, the student neither receives a scholarship nor can apply for IGA projects. In total, it is possible to study Ph.D. for 7 years, the dissertation must be defended (it is not enough to only submit) within 7 years from the beginning of the study.

To be admitted to the defense, the student must:

Have published at least 1 first-author work in an international impacted journal.
Have completed all exams from ISP subjects.
Undergo an international internship long at least 1 month. This stay does not have to be continuous, 4 1-week international conferences or other trips abroad are also valid.
Attend an English student conference, which takes place at UCT 3 times a year (March, June, November).

Individual Study Plan (ISP)

Although the deadline for creating the ISP in the school information system (SIS) is usually the end of September, the semester at UCT and the semester at FIT CTU already start during September. Therefore, it is recommended to create the ISP no later than the end of the first week of September so the student can start attending the lectures already in the winter semester of the first year.
Since the subjects in the ISP are related to the DSP areas (see further), it is necessary to think about the ISP soon enough and not leave it until the last minute.
Select at least two subjects from the module A and the remaining from the module B. Within the module B, it is possible to choose master's subjects from other faculties of UCT or other universities.
It is necessary to verify with the course guarantor that the selected course is indeed taught in the given semester. The information in school information systems may not be accurate! Another reason not to leave the ISP until the last minute, as communication with instructors may take some time.
Students put the list of subjects in the ISP into the SIS at the beginning of their studies. Then, the tutors check the ISP and forward it for approval to the subject area board. Both students and tutors will be timely invited to these actions by email.
Students do not enroll in the subjects in the ISP in the SIS. This also applies to master's subjects listed in the ISP.
Doctoral subjects are not scheduled in the SIS! Before the beginning of each semester, the student must contact the course guarantor to find out the date, time, and location of the teaching.
At the beginning of each semester, students will be asked to send a list of courses they will be attending at FIT CTU that semester. This list will be provided to FIT CTU, they will enroll the student to the course.
The prerequisite for the doctoral subject Algorithms of Computational Genomics is the completion of the master's subject Efficient Text Searching. If the student has not completed Efficient Text Searching, it is necessary to go through this subject first, however, it is not necessary to include it in the ISP (then the student does not have to take an exam from it). If the student wants to attend Efficient Text Searching, it is necessary to contact the guarantor of the subject as soon as possible!
The prerequisite for the doctoral subject Text Mining from the module A is the course Information Retrieval, which belongs to the module B. Since Text Mining is taught in the winter term and Information Retrieval in the summer term, the student will get to Text Mining in the 2nd year of study at the earliest.

State Doctoral Exam (SDZ) and Doctoral Study Subjects (ISP)

The ISP and the SDZ areas are closely linked. In fact, it is necessary to consider the choice of SDZ areas already when creating the ISP and to choose appropriate courses.
The SDZ areas must be specified both when filling out the evaluation in the e-doctorand system (usually after the 2nd year) and in the application for the basic part of the SDZ.
The connection between the course and the SDZ area does not mean that the student will be examined from this course. At the SDZ, broader knowledge in each area is verified.
For example, if a student does not have sufficiently strong knowledge of bioinformatics, he can, upon the agreement with the supervisor, instead of Systems Biology enroll in a suitable master's subject, such as Genomics: Algorithms and Analysis or any other. During the SDZ, the knowledge will be verified within the scope acquired during the PhD studies.
Similarly, for the choice of the Chemoinformatics SDZ area, it is not necessary to complete the DSP subject Advanced Chemical Informatics and it is possible to choose the master's Course Computational Drug Design.
In summary, at the SDZ the student is tested on the broader knowledge that he/she started to acquire during his/her master's studies and further acquired during his/her doctoral studies.
Prior to the SDZ, we recommend that students contact the examiners of their areas to discuss the content of the exam.

Access to Buildings and Information Systems

To arrange access to the FIT CTU buildings, the following needs to be arranged within 14 days before the beginning of the semester at UCT:
1. You need to have an ISIC or UCT student card. Information on how to obtain it can be found here.
2. In person visit the CTU Card Centre, tell them you are from bioinformatics at the UCT and that you will have courses at FIT.
3. For a fee of 50 CZK, access to FIT CTU will be uploaded to your card.
4. You will also receive a username for KOS (see below).
5. At this time, there can be many people there, so it is recommended to make a reservation in advance to avoid unnecessary waiting in line.
At the UCT, the information system SIS is used, at the FIT CTU the name of the system is KOS.
Supervisors from the UCT have a login to SIS. Supervisors outside the UCT do not have a login, but the UCT always sends them an email with a link for necessary actions (approval of ISP, annual student evaluation, etc.). Supervisors do not have access to KOS, nor do they need it.
The student receives a login to SIS upon the enrollment in doctoral studies.
Students and KOS

Students must have an account in the KOS for two reasons: 1. so that the examiner sees that they are enrolled in his course and he can insert their grade 2. so that they can see the course materials (which are stored in a different system, but there is also a need for a FIT username and password).
Regarding the access to the KOS, students will be invited at the beginning of the first year by the DSP guarantor to provide personal information, based on which their KOS login will be established.
Nothing happens after the KOS login was established, you may not even be notified by email!
Students are introduced into KOS at FIT by Mrs. Fryčová, direct any questions regarding the procedure to her.

Supervisor

If the thesis supervisor is from the FCHT UCT, then they can be a supervisor if they hold the title of associate professor or professor. If they are not an associate professor or professor, but have a Ph.D., then they must be approved for the specific topic by the Scientific Board (VR) of FCHT. The approval takes place at a VR meeting after the student registers for the specific topic. The supervisor is approved for only one specific topic. For approval by the VR, the supervisor will be asked by the DSP guarantor to submit a CV on a prescribed form.
If the thesis supervisor is from the Academy of Sciences, then two situations can occur:
1. The respective institute of the CAS has a "Partial Agreement on Mutual Cooperation in the Implementation of Doctoral Study Programs" with the "Bioinformatics" program. Then the thesis supervisor can be a supervisor with conditions on their titles corresponding to point 1. The DSP Bioinformatics has this agreement with the following institutes of the CAS: IOCB, IMG, MBÚ, FGÚ, ÚEM, BTÚ, and ÚEB.
2. The respective institute of the CAS does not have a "Partial Agreement on Mutual Cooperation in the Implementation of Doctoral Study Programs" with the "Bioinformatics" program. Then the thesis supervisor from that institute of the CAS can only act as a specialist-supervisor and the student must have a formal supervisor assigned from the Institute of Informatics and Chemistry of the FCHT UCT.

Scholarship

The details regarding PhD scholarships and other funding opportunities for doctoral studies are clearly described on this university page. All scholarships are tax-free, hence net.

Affiliation

If it does not concern actual cooperation between UCT and CAS, doctoral students working at CAS institutes are not required to have UCT affiliation on publications.

International Students

International students can study in the DSP Bioinformatics according to the following rules:

Enroll in the English DSP Bioinformatics. They pay a significant fee (65,500 CZK/year) and do not receive a scholarship. A very nonsensical and counterproductive limitation, dictated by university law.
They are admitted to the Czech DSP Bioinformatics under the following conditions:
1. Enroll in the first semester of the English DSP. They pay an administrative fee of 2,000 to 3,000 CZK for the first semester and do not receive a scholarship during this time. In the first semester, the student completes a Czech language course at UCT, ending with an exam.
2. At the beginning of the 2nd semester, the doctoral student transfers to the Czech DSP with all its benefits (no tuition fees, receives a scholarship, can apply for IGA projects, etc.). It is clear that the student will not learn Czech in one semester, therefore lectures in the Czech DSP are taught in English.

International students must have health insurance arranged during their stay in the Czech Republic. The rules are quite complex, dynamically changing, and the most qualified people to contact are always the HR staff of the respective institution. The rules are described in more detail in this document, here only in outline:

If the student only receives a scholarship and is not employed, for example, on a GAČR or other project:
1. If the student is from the EU and is under the age of 26, then the state pays their insurance in their home country. This is transferred from the home country to the country of stay upon request, so they do not have to pay anything in our country.
2. If the student is not from the EU, they must pay for insurance themselves.
If the student is employed on a grant, then the health insurance is paid from their salary and they do not have to pay anything else.

Annual Evaluation of the Doctoral Student

Every year in September, students submit a final report in the e-doctorand module in SIS, where they describe their activities throughout the year.
Students will be invited by email from the school to complete the report.
First-year students also submit this report and describe, for example, their diploma project or other interesting activities.
More detailed information about what is included in the annual evaluation can be found on these school pages.
Based on this report, the doctoral student's performance is scored each year. The awarding of points is governed by the rules described in the document "Overview of the Point Evaluation of DSP Students' Results at UCT Prague," which can be found on the page https://www.vscht.cz/studium/doktorske-studium. On the same page, you can find the point evaluation of impacted journals and other important documents.

More Information

For more detailed information about the Ph.D. program, please visit the Ph.D. study pages at UCT, and information for current doctoral students is available here.