Adobe Systems
Biomolecular Chemistry
and Bioinformatics (BINFO)
National Centre for Biomolecular Research
Guarantor: prof. Mgr. Lukáš Žídek, Ph.D., lzidek@chemi.muni.cz, room C04-126
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Adobe Systems
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BINFO PhD program Scientific board
•Internal members:
̶Assoc. Prof. Mgr. Lukáš Žídek, Ph.D. (Chair)
̶Assoc.prof. RNDr. Michaela Wimmerová, Ph.D.
̶Assoc. doc. Mgr. Lumír Krejčí, Ph.D.
̶Assoc. prof. RNDr. Vladimír Sklenář, DrSc.
̶Assoc. doc. RNDr. Radka Svobodová, Ph.D.
̶Assoc. prof. RNDr. Jiří Šponer, DrSc.
̶Assoc. prof. Mgr. Richard Štefl, Ph.D.
̶Assoc. doc. Mgr. Lukáš Trantírek, Ph.D.
̶Assoc. prof. Mgr. Štěpánka Vaňáčová, Ph.D.
•External members:
̶prof. Ing. Richard Hrabal, CSc. (Praha)
̶prof. RNDr. Michal Otyepka, Ph.D. (Olomouc)
̶Prof. Mgr. Daniel Svozil, Ph.D. (Praha)

As PhD you should:
• understand theories, concepts, and methods that represent current trends in structural biology
and bioinformatics
•become independent expert
• independently design and conduct research in all its stages
• interpret research outcomes and present them at international conferences
• write a research paper and publish it in an impacted international scientific journal
• teach/supervise students … to become a science leader once
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Milestones and deadlines
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1. 6. 2023 – 20. 9. 2023
Student’s semestral plan
15. 6. 2023 – 30. 9. 2023
Supervisor approves
1. 9. 2023 – 07. 10. 2023
Scientific board/chair approves
1. 12. 2023 – 31. 1. 2024
Student’s feedback
15. 12. 2023 – 15. 2. 2024
Supervisor evaluates
Anytime
Scientific board/chair evaluates
• Research project plan – 1st year
(max 1 page describing background, objectives, methods, and timeline).
• State Doctoral Exam (SDE/SDZ) – 2nd to 4th year (award)
• Thesis defense – 4th to 5th year (award) = standard time (4+1)
or later … extended = 8+1 (9th year only exceptions – dean must approve)

Studies roadmap – Mandatory duties
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• (FGP) seminars during whole regular study (not in combined study)
• Semesters 1-4 (first 2 years of study) - research project + theoretical courses,
• general requirements for all astudents in the programme (please see detailed requirements for the
Individual Study Plan in the detailed table below):
Mandatory duties: checked by Dean´s Office
Code
Title
XD100
Ph.D.thesis/ Příprava dizertační práce
Enrolled every semester during entire studies, recommended 20-25 ECTS for semesters 1-4, 30 ECTS
for semesters 5-8, 20 ECTS for semesters 9+
CB060
NCBR seminar/ Seminář NCBR
Obligatory seminar for all semesters of full-time study mode (with exceptions of stay abroad)
CB100
TAC/ Thesis Advisory Committee
Standard tool to provide individual quality assessment of PhD candidates, mandatory, to be enrolled
in 1st,4th-5th, 7th, 9th, 11th semester)
C7777
Handling chemical substances/
Zacházení s chemickými látkami
Enrolled every year of study, every autumn semester
CB030
Teaching Assistance/Pomoc při výuce
See table for details, maximum 150 hours in total during studies
XD106
Lecture in the foreign Language/
Odborná přednáška v cizím jazyce
Minimum once during studies
XD110
Placement Abroad/ Zahraniční pracovní pobyt
Minimum 1 month stay, min,1-time during studies , requirement given by law
C9870
Zpracování a prezentace vědeckých dat/ Processing and presentation of scientific data
Mandatory subject

Adobe Systems
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CB060/CC060 NCBR seminar
̶To practice the ability to present results in the form of a lecture
̶ To provide active feedback (discussing, asking questions) to other presenting students and to
critically evaluate their presentations.
̶ First 4 years as a student erolled in a course (credits), then as a community member
̶ Presentations of local structural biology experts and guests
̶ Great opportunity to present own work in front of the public
̶ Become a member of local scientific community

Adobe Systems
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CB100 Thesis Advisory Committee (TAC)
̶A tool to help PhD candidates make decisions, solve problems, prepare for the defense
̶Scientific board decided to implement TAC in December 2021 to help students to:
̶1st year: set up your doctoral project plan (1 meeting during 1st year)
̶4th/5th year: get your thesis finished in the standard study time of 4+1 years
•(1 meeting before the end of 4th year or beginning of 5th year)
̶6th year: get your thesis finished as soon as possible (1 meeting during 6th year)
̶7th/8th year: get your thesis finished as soon as possible (meeting every semester)
̶TAC report templates provided by PhD coordinator
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student + supervisor + at least 2 independent scientists

Adobe Systems
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CB030/CC030 Teaching Assistance
̶ 2 semesters teaching or 3 semesters co-supervising undergraduate students
̶ Credits given by the course guarantor, not by your supervisor
̶ When you enroll, contact the course guarantor and inform him/her, how you fulfill your duty
(which course you teach, how many hours, to what extent, which undergraduate student works under
your supervision, in which group)
̶ Credits: 2 for co-supervision, 3 for each hour of full-time, contact teaching
̶ Semesters, not credits count as the requirement (as an exception, a large load of teaching in one
semester can be accepted as completion of the duty)
̶ Do not select any other code when enrolling (XD102 or S5009)
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State Doctoral Exam (SDE)
•• prove general knowledge of structural biology and bioinformatics
•(answering shortly questions common for all students)
•• prove deeper insight into a narrower area related to the PhD thesis (scientific discussion)
•• students´presentation of his/her PhD topic (if taken in advance)
•• motivated by a stipend (currently 5000 CZK, if evaluated by A,B,C)
•• apply ASAP
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Thesis defense
•Thesis:
•• student must be the first author of at least one publication
•• student’s contribution must be stated
•• if the student co-authored at least 2 papers - comprehensive introduction and commentary on
papers
•• if there are less than 2 publications – monography, use templates provided by the university
•Defense:
•• student presents major results/achievements in 20 min, supervisor reads his/her evaluation of
the student,reviewers read their reports, student answers questions, discussion follows
•        SDE and defense applications via IS (Iva Klimova)
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