Experimental biology of plants 

Student Obligations

The conditions and criteria for doctoral studies are based on the following obligations:

Hard skills

During the first two years of study, students are required to take at least three vocational courses focused on hard skills. These courses can take the form of standard semester courses, summer schools or specific intensive courses.

A recommended list of hard skills courses is available below, but other relevant courses can be selected from the course catalogue.

Summer schools and short-term vocational courses that exceed 10 hours of instruction and are equivalent in intensity and focus to standard courses are also accepted. Course offerings are published in the News section, but other relevant courses may be selected. Participation in a summer school or specific course is subject to the approval of the instructor and the program sponsor. Recognition of course completion as part of the hard skills requirements is at the discretion of the program sponsor or his/her designee. It is recommended that the possibility of course recognition be consulted prior to taking the course.

Hard skills

Code

Course Name

Lecturer

Language

Focused on plants CZ

Bi8240

Plant genetics

J. Řepková (Mandáková)

CZ

 

Bi8080

Plant molecular physiology 

M. Šámalová

CZ

 

Bi8080c

Plant molecular physiology - practice

M. Šámalová

CZ

 

Bi8180

Physiology and cultivation of algae and cyanobacteria

P. Váczi

CZ

 

Bi8180c

Physiology and cultivation of algae and cyqanobacteria- practice

P. Váczi

CZ

 

Bi5880

Advanced methods in induced chlorophyl fluorescence

M. Barták

CZ

 

Bi5880c

Advanced methods in induced chlorophyl fluorescence- practice

M. Barták

CZ

 

Bi0321

Plant Polar Biology

M. Barták

CZ

 

Bi8004

Advanced Palnt Cell Biology

M. Pernisová

CZ

 

C7860

Plant Biochemistry

Lochman

CZ

 

Bi7160

Mineral Nutrition of Plants

V. Gloser

CZ

 

Bi6570

Plant microevolution and speciation

Zedek

CZ

 

Bi9090

Evo-devo plant biology

Zedek

CZ

 

 

 

 

 

General CZ

CG010

Proteomics

Zdrahal

CZ

 

CG020

Genomics

Hejatko

CZ

 

CG080

Methods in genomics

Fajkus

CZ

 

CG090

Metods in proteomics

Zdrahal

CZ

 

C7230

Fluorescence methods in life sciences- a journeyfrom molecules to cells 

Hofr

CZ

 

Bi9410c

Structural Biology- practice

Damborsky

CZ

 

 

 

 

 

Focused on plants EN

Bi0008

Principles Of Water And Nutrient Use By Plants

Gloser

EN

 

FALR1_12

Production of Medicinal Plants

Dvorska

EN

 

S2011

Hormones in plant development

Boisivon

EN

 

Bi8030en

Production Plant Biology

Bartak, Vaczi

EN

 

C7861

Plant Biochemistry

Lochman

EN

 

Bi0323

Experimental Plant Biology

Bartak

EN

 

Bi2002en

Methods in plant cytogenetics and cytogenomics I. - practical course

Mandakova

EN

 

Bi2004en

Methods in plant cytogenetics and cytogenomics II. - practical course

Mandakova

EN

 

 

 

 

 

General EN

C9095

RNA metabolism

Vanacova

EN

 

CG920

Genomics

Hejatko

EN

 

CG910

Proteomics

Zdrahal

EN

 

CG980

Methods in genomics

Fajkus

EN

 

CG990

Methods in proteomics

Zdrahal

EN

 

Bi9690en

Synthetic Biology

Riha

EN

Soft skills

During the first two years of study, students are obliged to attend at least one professional course or training focused on the development of soft skills. These activities may focus on presentation and communication skills, teamwork, management and leadership skills development or, for example, professional competences in bioinformatics and biostatistical data processing.

Courses can be taken within the offer of the Centre for the Development of Educational Competences (CERPEK MU), the PhD Academy of the South Moravian Innovation Centre, or other educational institutions, including summer schools and short-term training courses.

In the case of courses that are not listed in the MU course catalogue or the recommended list (see link), it is necessary to consult their suitability with the supervisor and programme guarantor or his/her designee before taking them.

Soft skills

Code

Course Name

Lecturer

Language

Notes

Biostatistics or Bioinformatics

E5540

Biostatistics – basic course

Dusek

CZ

General introduction to the biostatics.

 

E5540c

Biostatistics - practice

Dusek

CZ

General introduction to the biostatics - practice.

 

Bi7560

Introduction to R

dr. Kintrová

CZ

Good for beginniners in R.

 

E7527

Data analysis in R

Budinska, dr. Smetanová

CZ

Good for beginniners with basic knowledge of R.

 

E8600

Multivariate methods

Jarkovsky

CZ

Needs basic knowledge of R.

 

Bi1121

Data analysis in R for experimental and molecular biology

Ovesna

CZ

Good for beginniners in R.

 

Bi1121c

Data anylsis in R for experimental and molecular biology - practice

Ovesna

CZ

Good for beginniners in R - practice.

 

Bi9680en

Artificial Intelligence in Biology, Chemistry, and Bioengineering

Damborsky

EN

Focuses to AI, involves also introduction to Python.

 

Bi9680enc

Artificial Intelligence in Biology, Chemistry, and Bioengineering - practice

Damborsky

EN

Focuses to AI, involves also introduction to Python - practice.

 

M7DataSP

Advanced Data Science Practicum

Šimeček, students, guests from industry

CZ

Needs basic knowledge of Python.

 

 

 

 

 

 

General

S4002

Law, Ethics and Philosophy of Science

Havlis

EN

 

 

C4866

Discover the science - Scientific knowledge and thinking

Havlis

EN

 

 

C4868

Discover the science - Science and society

Havlis

EN

 

 

S4010

Science Communication Course: Present Your Research Results with Confidence

Hejatko

EN

The goal is to teach students how to prepare effective presentations.

 

XS450a

Communication skills training

Vrtala

EN

The aim is to improve students' ability to interact and communicate (ie listening and speaking) with people.

 

VLAW051

Academic Writing

Dvorackova LF

EN

Focuses on better understanding of English-language academic and science writing cultures.

 

S4001

International Performance

Stepanek

EN

Introduction to the different approaches in presentation of scientific outcomes.

 

SOe200

Introduction to Project Management and Writing

Stepanek

EN

Introduction to project design, management, and writing.

 

Bi3112

Science Writing Workshop

Nekola

EN

Participants must at the start of the course have some type of completed scientific analysis which they ultimately plan on submitting to a peer-reviewed journal.

 

Bi1151en

Effective Science Communication: Written and Graphic Skills

Harnos

EN

Explores written and graphic communication in science.

 

ILLU01

Illustration in science – actractive and comprehensive graphics  visualization in research and education

Hofr

CZ

On-line. Focuses on graphical design a data visualization.

 

FR_EL

FRESHERS: Skills for Research Careers

Various (>8)

EN

On-line. Overall picture of the topics that researchers face (financing research and grant opportunities, publication ethics, communication of science and research results promotion).

 

 

 

 

 

 

English

Bi0077

English for Plant Biologists

M. Barták

EN

 

 

JAD01

Advanced English for PhD studies (C1)

Coupkova

EN

 

 

JAD02

Advanced English for PhD studies (C1)

Coupkova

EN

 

Specialized seminar ExPBio

Students participate in specialized seminars focused on the presentation of the latest research findings, not only in the field of plant biology. Recommended activities include seminars organized at the Faculty of Science of MU or within CEITEC MU, such as Mendel Centre Seminars in Life Sciences (IS MU: S2009) Life Sciences Seminar (IS MU: S5030, S5035, XD010, XD011, Bi0011), Life Science PI Seminar (IS MU: S5020), NCBR Seminar (IS MU: CB060, CC060), Doctoral Seminar IEB (IS MU: Bi0100, Bi0101) or the Seminar of the Institute of Experimental Biology FGP (IS MU: C9950).

It is also possible to attend professional lectures organised outside Masaryk University, within other academic and research institutions. However, participation in lectures within conferences is not counted among the lectures attended; only individual professional lectures organised by research institutes are recognised.

Credit for the course Specialised Seminar - ExPBio (IS MU: C0030) may be awarded on the basis of a list of completed lectures submitted by the student. The list may be verified by the programme guarantor or his/her designee against the official electronic attendance register kept for seminars organised by Masaryk University.

To receive credit, student is obliged to:

- full-time students must attend at least 8 lectures per semester,

- combined forms of study at least 4 lectures per semester.

Template for confirmation of student´s participation (download here):

  • Lecture date
  • Place of venue
  • Name of speaker
  • Lecture title
  • Brief content of lecture (one sentence)

The completed template should be placed in the course "Submissions/Odevzdávárna" at the end of each semester. After checking, credit will be given by the program guarantor.

International conferences

Students are obliged to present their research results in a form of presentation at least once during their four years of study at an international conference, forum or workshop. If you are attending an international conference abroad, please contact the guarantor and copy the PhD coordinator with the following information:

  • Title and website link of the event
  • Date of presentation
  • Place of venue
  • Name of speaker
  • Lecture title
  • Brief content of the lecture (in one sentence)

The guarantor will ensure that credit is awarded in the IS MU under the subject "Lecture in the Foreign Language" (IS MU: XD106).

Internship abroad

Completion of an internship abroad (at least 30 days)

During studies, the student is obliged to complete a foreign internship (IS MU: XD103) or alternatively a foreign professional practice (IS MU: XD110) of at least one month (in total for the duration of your studies), or in accordance with the requirements of national or university standards. The thematic focus of the internship or work experience must be related to the topic of the dissertation.

In exceptional and justified cases, the departmental board may decide on an alternative way of fulfilling this obligation, for example by active involvement in an international project for a minimum of two years.

Always contact the Mobility coordinator prior to departure to be infromed about the current documentation required before, during and after the internship.

Handling Chemical Substances

Students are obliged to take the course “Handling Chemical Substances” (IS MU: C7777) every semester for the entire duration of your studies.

ExPBio PhD Retreat

Students are obliged to attend and present their results at the ExPBio PhD Retreat every year. The detailed participation procedure is defined in the PhD Retreat guidelines. Full-time students are obliged to actively participate in the direct organisation of the Retreat. In justified cases, the program guarantor or his/her designee may decide on an alternative way of fulfilling this obligation. Upon completion of the Retreat, students are awarded “ExPBio PhD Retreat” credit (IS MU: C0020) in the information system.

TAC - Thesis Advisory Committe

The establishment of a Thesis Advisory Committee (TAC) is a mandatory part of the doctoral studies. It serves to continuously monitor study progress in collaboration with external experts. The TAC is responsible for monitoring the progress of the thesis project, providing expert advice and support to both the student and the supervisor.

Credit is awarded to the student for completion of each TAC meeting in the MU Information System (IS MU:C0010).

Composition of the TAC

The student is responsible for the composition of the TAC in collaboration with his/her supervisor. Committee members are selected and appointed by the end of the first year of study. The TAC must include the supervisor and at least two other members who are not part of the supervisor's research group; at least one member must be external, i.e. outside the institution where the student is carrying out his/her doctoral research (e.g. Masaryk University, Institute of Biophysics of the CAS, etc.). The inclusion of a foreign expert is possible and considered beneficial. There is no upper limit on the number of TAC members. Any expert (internal or external) with relevant experience in supervising PhD students can become a member. The composition of the TAC is subject to the approval of the program guarantor or his/her designee and subsequently approved by the ExPBio Departmental Board.

TAC meetings

TAC meetings can be initiated by the student, the supervisor, the program quarantor or his designee. Participation of individual members is also possible by distance (online). The student is responsible for organising the meetings, including inviting the members and ensuring the submission of fully completed evaluation reports.

  • The first TAC meeting must take place no later than the end of the second semester and includes a research plan during the entire PhD study.
  • The second meeting should take place by the end of the fourth semester, unless required earlier, and includes the proposed goals of the dissertation thesis.
  • The third meeting is recommended during the seventh semester of study, unless required earlier, and includes the progress of the work and the final goals of the disseration thesis.
  • In addition to the three prescribed TAC meetings, additional TAC meeting may be convened by the supervisor, student, program guarantor or his/her designee any time during the course of study.
  • After the standard period of study (i.e., after eight semesters) or upon recommendation of the departmental board, the TAC must be expanded to include an additional external member and convened periodically on an annual basis or as needed.

TAC process

If necessary - two weeks prior the meeting, the PhD student or supervisor will send a non-public part of the documents to the PhD coordinator. The non-public part is not compulsory, but serves to better inform the TAC and the program guarantor about possible problems concerning the course of study. This section is completed separately by the PhD student and the supervisor and is used to discuss individual perspectives separately during the meeting.

One week prior to each meeting, the doctoral student will send all TAC members a written document - e.g. a draft PowerPoint presentation. Student may also include a summary of progress or a working version of the dissertation thesis, depending on the current state of the project.

Portions of the meeting without the PhD student or supervisor present are confidential and allow for open discussion of potential problems in the collaboration. In the event of a conflict of interest, ethical issues, or feelings of unequal status, the PhD student or any TAC member may request that the PhD coordinator attend the meeting.

TAC meeting structure:

  • Presentation by the PhD student (about 20 minutes) followed by a discussion with all TAC members.
  • Discussion between the PhD student and TAC members without the presence of the supervisor.
  • Internal discussion among TAC members without the doctoral student present.
  • Final summary and recommendations by the TAC Chair.

TAC cancellation and replacement of members

  • The TAC can be dissolved by a decision of the PhD student or the Departmental board. A new TAC must be formed ideally within one month. Transferring TACs should be the ultimate solution and should not be done more than once during the entire study.
  • Individual members can be replaced if necessary. The change must be approved by the discipline council.

TAC documentation

TAC meeting include:

  • Official documents, approved by all TAC members, the student and the supervisor.
  • If necessary, a non-public section to be completed separately by the student and supervisor. The non-public part can be completed and sent to the PhD coordinator at least two weeks before the TAC meeting. The PhD coordinator will inform the relevant members of the TAC or the program guarantor or his/her designee.

Mandatory documents for individual TAC meetings are available for download:

  • Minutes of the 1st regular TAC
  • Minutes of the 2nd regular TAC
  • Minutes of the 3rd regular TAC
  • Minutes of the Extraordinary TAC
  • Mandatory non-public part of the TAC report - student
  • Mandatory non-public part of the TAC report – supervisor

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