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 subject-area board (OR) is responsible for the proper execution of Ph.D. programme and its content. OR monitors and evaluates ongoing studies, approves individual study plans (ISP) and their changes, proposes the composition of committees for state doctoral examinations and committees for the defense of dissertation works, or approves opponents of dissertation works. OR meets once a year in January, urgent votes are resolved by 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 Ph.D. studies 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 not defended within 4 years, the student can switch to the combined study. Its length is 3 years and during this time, the student no longer 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 impact journal.
Have completed all exams from subjects from his/her individual study plan.
Undergo an international internship at least 1 month long. This stay does not have to be continuous, e.g., 4 week international conferences or other trips abroad are recognized.
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 consider the ISP no later than the end of the first week of September so that the student can start attending the respective 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 a bit about the ISP and not leave it until the last minute.
Select at least two subjects from module A and the remaining (up to four) from module B. Within module B, it is possible to choose master's subjects from other faculties of UCT or other universities.
It is necessary for the student to verify in time 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 not be very fast.
Students insert the list of subjects in the ISP into the school system at the beginning of their studies. Then the tutors check the ISP in the system and forward it for approval by 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! 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 subjects they will be attending at FIT CTU that semester. This list will be provided to FIT CTU, where the student will be counted in the subject.
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 a student wants to attend Efficient Text Searching, it is necessary to contact the guarantor of the subject as soon as possible and arrange it with him!
The prerequisite for the doctoral subject Text Mining from module A is the completion of the doctoral subject Information Retrieval, which belongs to module B. Since Text Mining is taught in the WS and Information Retrieval in the SS, the student will get to Text Mining at the earliest in the 2nd year of study.

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 choose appropriate subjects accordingly.
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 mentioned connection to the subject in the SDZ areas does not mean that the student will be examined in the scope of knowledge from this subject. At the SDZ, broader knowledge and overview in each area are verified.
For example, if a student does not have sufficiently strong knowledge of bioinformatics, they can, by agreement with the tutor, enroll in a suitable master's subject instead of a DSP subject, such as Systemic Biology or Genomics: Algorithms and Analysis or another. The knowledge will then be verified at the SDZ within the scope acquired during doctoral studies.
Similarly, for choosing the SDZ area of Chemoinformatics, it is not necessary to complete the DSP subject Advanced Chemical Informatics and a master's subject Computer-Aided Drug Design can be chosen instead.
In summary, at the SDZ, the student is examined from a broader range of knowledge, which they began to acquire during master's studies and further during doctoral studies.
Before the SDZ, it is recommended that the student contacts the examiners of their areas and arranges with them regarding the content of the areas during the exam.

Access to Buildings and Information Systems

To arrange access to the buildings of FIT CTU, the following needs to be done 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. Visit in person the CTU Card Centre, state that you are from UCT bioinformatics and that you will have subjects at FIT.
3. For a fee of 50 CZK, access to FIT CTU will be uploaded to your card.
4. During the visit, 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 UCT, the information system SIS is used, at FIT CTU the system KOS.
Tutors from UCT have a login to SIS. Tutors outside UCT do not have a login, but the school always sends them an email with a link for necessary actions (approval of ISP, annual student evaluation, etc.). Tutors do not have access to KOS, nor do they need it.
The student receives a login to SIS upon enrollment in doctoral studies.
Students and KOS

Students must be introduced into KOS for two reasons: 1. so that the examiner can enter their grade and see that they are enrolled in his subject and 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 establishment of access to 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 then be established at FIT.
Nothing happens after being introduced into KOS, 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

All scholarships are tax-free, hence net. It is necessary to distinguish between the case where the place of dissertation work is the FCHT UCT institute and when it is the CAS institute.

When the place of dissertation work is the FCHT UCT institute. The student's scholarship consists of the following items:
1. Fixed items
  1. Basic scholarship of 7,700 CZK/month. For each unfulfilled obligation, the scholarship is reduced by 500 CZK/month in individual years. The entire system is described in detail in the document "Determination of the Amount of Basic Doctoral Scholarship" on the page https://www.vscht.cz/studium/doktorske-studium/doktorske-stipendium.
  2. Teaching scholarship of 3,500 CZK/month. Allocated if the student participates in teaching/exercises in any subject, helps in guiding bachelor or master students, etc.
2. Variable items
  1. VIGA (Internal Scientific Grant Agency) project (see https://www.vscht.cz/veda-a-vyzkum/iga/viga)
    1. Project A1 - so-called disciplinary grant. This grant is submitted every year by the program guarantor (prof. D. Svozil), and within its framework, students are additionally paid a scholarship, the amount of which is derived according to the student's performance as calculated by the application http://edoktorand.vscht.cz. Typically, the reward ranges from 1,500 CZK/month to 2,500 CZK/month, for particularly high-performing students it can be up to 5,000 CZK/month.
    2. Project A2 - so-called research grant. It is a one-year project submitted by the student. Its purpose is for the student to learn how to formulate ideas and convert them into a grant application. The limits of claimable financial resources can be found in the document "Announcement of IGA Competition", and these are further specified by our faculty (FCHT). When submitting an application, it is necessary to follow the faculty rules! In addition to a scholarship of up to 5,000 CZK/month, the doctoral student can claim operational funds or travel expenses.
  2. Votoček's scholarship – the top 20 students at UCT receive an addition of 6,000 CZK/month.
  3. Other IGA projects, see https://www.vscht.cz/veda-a-vyzkum/iga. Students apply for specific social (SIGA) or pedagogical (PIGA) activities.
3. Employment contract. Some tutors can offer a partial or full employment contract or allow a partial contract outside the place of doctoral studies execution. This needs to be communicated with the tutor.
When the place of dissertation work is the CAS institute. The student's scholarship consists of the following items:
1. Fixed items
  1. Basic scholarship of 7,700 CZK/month. For each unfulfilled obligation, the scholarship is reduced by 500 CZK/month in individual years. The entire system is described in detail in the document "Determination of the Amount of Basic Doctoral Scholarship" on the page https://www.vscht.cz/studium/doktorske-studium/doktorske-stipendium.
  2. Teaching scholarship of 3,500 CZK/month. For students at CAS, it is very rarely allocated, the student must provide some UCT subject and the scholarship is paid only for months when the subject teaching takes place.
2. Variable items
  1. Research project VIGA. The student can apply for it only if they have at least 50% of points with the affiliation of the UCT workplace (affiliation does not have to be exclusive, i.e., it is possible to have two or more affiliations). If this condition is met, the doctoral student is not restricted in any way, i.e., for the duration of the project (1 year) they can improve their income by up to 5,000 CZK/month.
  2. It is not possible to apply for any other resources (PIGA, SIGA, Votoček's scholarship, etc.) at UCT.
  3. Some CAS institutes offer their internal grants, it is always necessary to inquire.
3. Employment contract. Some tutors can offer a partial or full employment contract or allow a partial contract outside the place of doctoral studies execution. This needs to be communicated with the tutor.

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.