Applicationfor!a! Doctoral!Programme!in!Biotechnology!/Bioteknologi (V...2 . 1. Programme Name . Eng: Doctoral Programme in Biotechnology Swe: Doktorsprogram i Bioteknologi . 2. Scientific

Application for a

Doctoral Programme in Biotechnology

2010-10-29 KTH School of Biotechnology

perake

Text Box

V-2009-024669 ENG, Revised

Doctoral Programme in Biotechnology

Programme Description


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1. Programme Name Eng: Doctoral Programme in Biotechnology Swe: Doktorsprogram i Bioteknologi 2. Scientific Field

Biotechnology is the integration of natural sciences and engineering in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services (European Federation of Biotechnology, 1980). Further, the United Nations Convention on Biological Diversity defines biotechnology as: "Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."

3. Overall Goals of the Doctoral Programme in Biotechnology The overall goals of the Doctoral Programme complies with the goals for the research education that have been layed down by the faculty of KTH: The aim is to provide the society with researchers who can contribute to the development of a sustainable society. The research students shall become independent and excellent researchers. After completed studies the research student in the Doctoral Programme in Biotechnology shall be able to:

• Describe and explain theories and empirical results within the area of specialization • Formulate concrete research questions within the area of specialization • Use scientific methods and develop new knowledge through own scientific studies • Critically analyze and evaluate used methods and results from own and others scientific studies • Present and discuss research results within the scientific community • Present research in a pedagogical manner outside the scientific community and in educational situations • Evaluate ethical aspects concerning research within the area of specialization and being able to act accordingly • Identify needs for new knowledge and have the ability and knowledge to initiate and lead research activities

4. Doctoral Programme Size and Student Recruitment 4.1 Estimated number of enrolled students. Under the six-year period between 2004-2009, 16 doctoral students were, on average, enrolled as new PhD students each year in Biotechnology (not including an average of 12 per year for the specialization area of Theoretical Chemistry). This translates to approximately 70 simultaneously active PhD students in the research education subject (sv. forskarutbildningsämnet) Biotechnology at the KTH BIO school. It could be expected that a

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similar number of students will also be enrolled each year in the planned Doctoral Programme in Biotechnology. However, the number of enrolled doctoral students will continue to be dependent on both the financial situation (faculty funding and external grants) and on available supervisor resources. 4.2 Student target groups. The target groups for the Doctoral Programme in Biotechnology are students with exams from Swedish or international undergraduate programmes, typically Master of Science programmes, in the areas of biological life sciences and biotechnology. 4.3 Admission Requirements. Eligibility to the Doctoral Programme in Biotechnology first involves the basic requirements for admission to research studies in general set forth by the Swedish Government (see "Högskoleförordningen", chapter 7, § 39):

1. a completed university exam at advanced level,

2. fullfilled course requirements of at least 240 ECTS, of which at least 60 ECTS are at advanced level, or

3. corresponding merits acquired through other procedures

Further, for admission to the Doctoral Programme in Biotechnology, the completed university exam or the advanced level courses should be in the subject area of biological life sciences or biotechnology.

In addition to these requirements, also special requirements for a particular specialization area may apply. These are described in the document "Study plan for the research education subject Biotechnology (see Appendix 1). When included, these requirements are deemed necessary for the students to benefit from the training, and may for example involve knowledge/skills from university studies in particular areas of importance for the subject area or language skills. The requirements are the same for students aiming for either doctoral or licentiate degrees.

4.4 Recruitment and enrollment of research students. Recruitment, eligibility control of students will be performed according to the procedures recommended by KTH: Text under länkar skall översättas till engelska. Det skall anges att om texten uppdateras skall de nya reglerna gälla för programmet. För aktuell version kan man gå till KTHs regelverk (ange länk). • Advertisment policy. See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/antagning/antagningsordning-for-utbildning-pa-forskarniva-vid-kth-1.27236 • Selection criteria. See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/antagning/antagningsordning-for-utbildning-pa-forskarniva-vid-kth-1.27236

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• Eligibility control process, exceptions etc. See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/antagning/antagningsordning-for-utbildning-pa-forskarniva-vid-kth-1.27236 • Main supervisor/co-supervisor(s). See: http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/handledning-studieuppfoljning/handledare-och-handledning-av-doktorand-1.27238 • Financial plan. A financial plan for the first two years should be presented at the time of submission of the admission documents. 4.5 Supervisor capacity. At present, more than 20 senior scientists at the School of Biotechnology comply with the formal requirements to act as main supervisors; i.e. holding at least a 50% full-time permanent employment at KTH and with academic merit levels of associate professor (docent) or higher (see Appendix 2). Further, a number of PhDs are active at the BIO School as senior scientists and some of them are likely promoted to associate professors within 5-10 years, and thus can act as main supervisors for licentiate or doctoral degree students. It can be estimated that three of the presently active eleven professors are retiring from their positions in the coming ten-year period (2011-2020). 5. Financing 5.1 Financing of key persons in the programme. The programme responsible person will be partly (ca. 20 % of an FTE) financed by the KTH School of Biotechnology. Main supervisors and course responsible persons, including the persons included in the programme steering committee, will be financed through a mixture of faculty support and external grants. 5.2 Financing of research students. Enrolled research students are expected to be financed mainly through external grants from various national and international sources, including The Swedish Research Council (VR), VINNOVA and EU as well as from industry and other private bodies (e.g. Knut and Alice Wallenberg Foundation, Wenner-Gren Foundation). In addition, the KTH School of Biotechnology has since 2008 an internal programme for appointment of "Excellence PhD students", with a background from the KTH Biotechnology education programmes. Selected students are given a four-year grant from the school to be used for the financing of a PhD student position (sw. "doktorandtjänst") with a main supervisor employed at the School of Biotechnology. At present, two/four students per year are selected, which are free to choose any main supervisor at the school. The plan is to continue this programme also after the introduction of the Doctoral Programmes at the School of Biotechnology (Biotechnology and Theoretical Chemistry and Biology). 6. Courses A 240 ECTS credits doctoral degree exam comprises a course part of 60 ECTS credits and a thesis part of 180 ECTS credits. Of the 60 ECTS credits of courses included, 60 % (=36 ECTS credits) need to be research level courses. A 120 ECTS credits licentiate degree exam comprises a course part of 30 ECTS credits and a thesis part of 90 ECTS credits. Of the 30 ECTS credits of courses

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included, 50 % (=15 ECTS credits) need to be research level courses. Research level courses given at KTH are classified into four different categories: (A) Advanced courses (B) Research skill courses (C) Broadening courses (D) Other courses The Doctoral Programme in Biotechnology includes a single research education subject; Biotechnology, with seven different specialization areas: (1) Biochemistry (2) Bioprocess Engineering (3) Molecular Biotechnology (4) Glycoscience (5) Gene Technology (6) Bioinformatics and System Biology (7) Nanobiotechnology For each of these specialization areas, a course package of obligatory (O) and recommended (R) courses has been assembled from the different categories of courses (A-D) (see Appendix 3). Obligatory courses should be given at least every second year. A few courses are obligatory for all specialization areas, and thus constitute common courses for the Doctoral Programme in Biotechnology. The total number of ECTS credits corresponding to obligatory courses (incl. conditionally obligatory courses) varies between 25.5 and 44.0, depending on the specialization area. The possibility to replace an obligatory course with an equivalent course shall exist, after approval from the programme responsible person and the Director of Postgraduate Studies. 7. Description of the Systematic Quality Assessment Activities The goal for the systematic quality assessment work is to secure that the education goals are fulfilled. 7.1 Programme steering committee. A doctoral programme steering committee, consisting of the programme responsible person, the director of postgraduate studies, two to three main supervisor representatives and one research student representative will be formed which in regular meetings (approximately bi-annually) will discuss quality aspects related to particular parts of the process, incl.: - the recruitment process - supervisor competence - the course/seminar activities, incl. written evaluations - thesis quality - student throughput - employability after examination 7.2 Supervisors forum. The supervisors within a particular specialization area or a group of specialization areas are recommended to meet at least annually in a specific forum for discussions about the doctoral programme, the courses, the quality of the research, supervisor issues and the progress of the research students.

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7.3 Courses and theses quality assessment. • All courses should preferably be subject to a written evaluation. • In addition to the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),

the following criteria, representing the present praxis and norm for the scientific field, should serve as guidelines related to the content and quality of doctoral and licentiate theses. Cases for which these guidelines for any reason are not considered applicable or relevant should be discussed with the director of postgraduate studies and the dean of KTH School of Biotechnology.

DOCTORAL THESIS

Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on four papers. • Normally, two of the included papers should either be already published or formally accepted for

publication ("in press") in international peer-reviewed scientific journals. Additional papers could be included as manuscripts, preferably as "submitted for publication" to international peer-reviewed scientific journals.

• The student should appear as first author on at least two of the papers, including one of the papers belonging to the "published or in press" category.

• For any paper included, his/her contribution should be significant and clearly identifiable. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at

least one senior scientist.

• In the case a thesis is based solely on manuscripts which are not already published or formally accepted for publication ("in press") in international peer-reviewed scientific journals, the thesis and the manuscripts should be pre-examined prior to printing, in addition to the main supervisor and at least one senior scientist, also by the faculty opponent and the evaluation committee.

Monography thesis (sv. "monografi") • Monography theses should be avoided. KTH has the outspoken policy that research results should

be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at

least two senior scientists and the director of post-graduate studies.

LICENTIATE THESIS

Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on two papers. • The included papers need not to be already published or formally accepted for publication ("in

press") in peer-reviewed international scientific journals. However, at least one manuscript should normally be included as "submitted for publication" to an international peer-reviewed scientific journal.

• The student should appear as first author on at least one of the papers included. • For any paper included, his/her contribution should be significant and clearly identifiable.

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• If the thesis includes one or more paper which are published or formally accepted for publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least one senior scientist.

• If the thesis does not include any paper which is published or formally accepted for publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least two senior scientists.

Monography thesis (sv. "monografi") • Monography theses should be avoided. KTH has the outspoken policy that research results should

be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at

least two senior scientists and the director of postgraduate studies.

7.4 Assessment of the infrastructure available for students within the doctoral programme. The School of Biotechnology has two sites for laboratory work; the AlbaNova University Center and the KTH facilities of which the latter resides within the Science for Life Laboratory hosted in the Karolinska Science Park house (Solna). Both these laboratories represent modern laboratories appropriately equipped for biological life science experiments, involving handling, storage and destruction of biological materials (fume hoods, temperated incubator rooms, refrigerator and freeze rooms, autoclaves etc.). In addition, the instrumental standard is relatively high, exemplified for example by instrumentation for (i) measurements of biomolecular recognition (biosensors, flow cytometers), (ii) high throughput sequencing of nucleic acids (DNA sequencers), (iii) microarray fabrication (nucleic acids and proteins) and scanning, (iv) DNA amplification (PCR instruments), (v) spectrophotometers, (vi) biosample centrifugation, (vii) biomolecule purification (chromatography equipment), (viii) mass determination (mass spectrometers) and (ix) fermentors of different scales (2 to 300 litres) for cell culturing. All PhD students are provided with an office work place, a computer and standard office facilities (printer, fax, scanner, telephone, etc.). Pentry spaces are available for cooking of own food. The KTH School of Biotechnology provides standard administrative services to PhD students, such as administration of salary payment, insurances, vacations, parental leaves, etc. A human resources (HR) responsible function is available. The services of the large KTH central library is available to all students. KTH Bio school-related research education matters are handled by both local and more central functions: • Programme responsible person • The Chemistry and Biotechnology (KKB) Office (joint facility between CHE and BIO schools) • The local research education administration responsible persons • The director of postgraduate studies 8. Local, National and International Networks On the local level, the regularly arranged literature seminar courses in which research topics of general and broad interest are presented and discussed in a plenum, serve as an important forum for cross-disciplinary interactions, scientific and social networking and competence broadening. For the indicated specialization areas, it will be obligatory to participate in at least one full-year rounds of

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this type of seminar series. There are no formal (i.e. agreement regulated) and repeatedly re-occuring exchange programmes with international universities associated to the doctoral programme. However, when motivated from the research project, enrolled PhD students are encouraged to visit other research groups and laboratories for different time periods, for example to learn a new technique or to perform collaborative experiments. Large EU consortia and center environments are excellent milieus for establishing networks both between academic researchers and between academic researchers and industry. There are presently (autumn 2010) a number of active network-promoting projects or centers at the KTH School of Biotechnology (see Appendix 4). The effort is to continue these initiatives to be participating in larger consortia, to provide research students within the doctoral programme in Biotechnology with networking opportunities.

9. Connections Between the Doctoral Programme and the School Development Plan and the Rector Contract

The Doctoral Programme will use Excellence student positions as one source of financing for enrolled PhD students. The financing of these positions is in part linked to the present and future Rector Contracts (Rector Contract). The introduction of specialization area-specific course packages is in line with the long term efforts of the BIO school to secure the quality of the research education (BIO school Strategy Plan 2009-2012). The Doctoral Programme relies on senior scientists as course responsible persons and as supervisors. The financing of such positions will continue to rely on a mixed source of funding, incl. external grants and various categories of faculty funding such as (in Swedish) GRU, Verksamhetsbas-stöd, FAKIR, included in the annual Rector Contracts (Rector Contract). The integration of the research education activities at the new campus Science for Life laboratorium within the organization of the Doctoral Programme in Biotechnology, is in line with the planned efforts to maintain a unified organization of the BIO school, also after being geographically separated to two sites (BIO school Strategy Plan 2009-2012).

APPENDIX 1: Study Plan for the Research Education Subject "Biotechnology"

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DOCTORAL PROGRAMME IN BIOTECHNOLOGY

APPENDIX 1

Study Plan for the Research Education Subject

Biotechnology



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Table of contents

Section Page 1. Subject Description and Goal for the Education 3

2. Specialization Area of Biochemistry 5

3. Specialization Area of Bioprocess Engineering 7

4. Specialization Area of Molecular Biotechnology 10

5. Specialization Area of Glycoscience 13

Specialization Area of Gene Technology 16

7. Specialization Area of Bioinformatics and Systems

Biology

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8. Specialization Area of Nanobiotechnology 21

9. Eligibility and Selection 24

10. Examina and Tests in the Education 25


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tudy plan for the research education subject Biotechnology, at the KTH School of Bioptechnology. Common regulations and guidelines for research education studies at KTH are available in the university´s central regulations collection "KTH handbook: Regulations for education at research level". The present study plan for education at

research level in the subject Biotechnology shall be seen as a complement to the common regulations by the following subject specific specifications.

1. Subject Description and Goal for the Education

1.1 Scientific field

Biotechnology is the integration of natural sciences and engineering in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services (European Federation of Biotechnology, 1980). Further, the United Nations Convention on Biological Diversity defines biotechnology as: "Any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use."

1.2 Specialization areas

The specialization areas within the research education subject Biotechnology are:

- Biochemistry - Bioprocess Technology - Molecular Biotechnology - Glycoscience - Gene Technology - Bioinformatics and Systems Biology - Nanobiotechnology

1.3 Overall goals for the education

The overall goals of the Doctoral Programme complies with the goals for the research education that have been layed down by the faculty of KTH: The aim is to provide the society with researchers who can contribute to the development of a sustainable society. The research students shall become independent and excellent researchers. After completed studies the research student in the Doctoral Programme in Biotechnology shall be able to:

S


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• Describe and explain theories and empirical results within the area of specialization • Formulate concrete research questions within the area of specialization • Use scientific methods and develop new knowledge through own scientific studies • Critically analyze and evaluate used methods and results from own and others scientific studies • Present and discuss research results within the scientific community • Present research in a pedagogical manner outside the scientific community and in educational situations • Evaluate ethical aspects concerning research within the area of specialization and being able to act accordingly • Identify needs for new knowledge and have the ability and knowledge to initiate and lead research activities

2. Specialization Area of Biochemistry 2.1 Description of the specialization area Research and postgraduate studies in Biochemistry include general biochemistry, in particular the application to technical processes and systems. This involves an increased understanding of the function and regulation of cellular components, and of the molecular processes and structures that constitute the basis for various forms of life.

2.2 Present research topics Present research topics include for example various aspects on basic and applied enzymology, including the investigation of the molecular characteristics leading to observed traits as well as a theoretical modelling and practical engineering of enzymes and substrates at the molecular level to achieve desired performances and activities in different milieus and biotechnological applications. The research also includes ecological biotechnology for development of environmentally friendly methods as alternatives to toxic biocides in forestry and agriculture. 2.3 Structure of the education The education in Biochemistry at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Biochemistry. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 2.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In the case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be


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defended at a dissertation at the end of the studies (see section 2.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 2.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level. Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the specialization area Biochemistry students need to have acquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - BB1030 Microbiology - BB1080 Biochemistry, theory - BB2020 Molecular Enzymology These so called special admission requirements concerning courses or oher qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 2.5 Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),

the following criteria, representing the present praxis and norm for the scientific field, should serve as guidelines related to the content and quality of doctoral and licentiate theses. Cases for which these guidelines for any reason are not considered applicable or relevant should be


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discussed with the director of postgraduate studied and the dean of KTH-School of Biotechnology.

- DOCTORAL THESIS -

Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on four papers. • Normally, two of the included papers should either be already published or formally

accepted for publication ("in press") in international peer-reviewed scientific journals. Additional papers could be included as manuscripts, preferably as "submitted for publication" to international peer-reviewed scientific journals.


• For any paper included his/her contribution should be significant and clearly identifiable. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also

by at least one senior scientist.

• In the case a thesis is based solely on manuscripts which are not already published or formally accepted for publication ("in press") in international peer-reviewed scientific journals, the thesis and the manuscripts should be pre-examined prior to printing, in addition to the main supervisor and at least one senior scientist also by the faculty opponent and the evaluation committee.

Monography thesis (sv. "monografi") • Monography theses should be avoided. KTH has the outspoken policy that research results

should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also

by at least two senior scientists and the director of postgraduate studied.

- LICENTIATE THESIS -

Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on two papers. • The included papers need not to be already published or formally accepted for publication

("in press") in peer-reviewed international scientific journals. However, at least one manuscript should normally be included as "submitted for publication" to an international peer-reviewed scientific journal.

• The student should appear as first author on at least one of the papers included. • For any paper included his/her contribution should be significant and clearly identifiable. • If the thesis includes one or more paper which are published or formally accepted for

publication ("in press") in an international peer-reviewed scientific journal, the thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least one senior scientist.



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by at least two senior scientists and the director of postgraduate studies.

3. Specialization Area of Bioprocess Engineering 3.1 Description of the specialization area Research and postgraduate studies in Bioprocess Engineering involves research in all parts of the bioprocess and the aim is to integrate both the biological and engineering aspects of the subject. The process design criteria are directed to safe, efficient and environmentally sustainable processes for production of important commercial products and services. 3.2 Present research topics Present research topics are directed to the design of both procaryotic and eucaryotic cells to tailor-made organisms for specific purposes. Examples are organisms that can take up carbon rich waste material, organisms that produce products of high quantity and quality, organisms that can perform new and specific biocatalytic processes and organisms that can remove toxic substances form polluted water. These organisms are integrated into an optimisation of cultivation media as well as the design and control of the bioreaction, recovery and purification process steps. 3.3 Structure of the education The education in Bioprocess Engineering at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Bioprocess Engineering. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 3.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of postgraduate studies before these can be part of an individual course package. In case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 3.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 3.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should


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correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level. Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the specialization area Bioprocess Technology students need to have acquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - BB2480 Energy and environment - BB2450 Cell Factory - BB2XXX Bioprocess Design These so called special admission requirements concerning courses or other qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 3.5 Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),

the following criteria, representing the present praxis and norm for the scientific field, should serve as guidelines related to the content and quality of doctoral and licentiate theses. Cases for which these guidelines for any reason are not considered applicable or relevant should be discussed with the director of postgraduate studied and the dean of KTH-School of Biotechnology.

- DOCTORAL THESIS -


accepted for publication ("in press") in international peer-reviewed scientific journals.


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Additional papers could be included as manuscripts, preferably as "submitted for publication" to international peer-reviewed scientific journals.




• In case a thesis is based solely on manuscripts which are not already published or formally accepted for publication ("in press") in international peer-reviewed scientific journals, the thesis and the manuscripts should be pre-examined prior to printing, in addition to the main supervisor and at least one senior scientist also by the faculty opponent and the evaluation committee.














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4. Specialization Area of Molecular Biotechnology 4.1 Description of the specialization area

Research and postgraduate studies in Molecular Biotechnology include engineering of microorganisms and their biomolecular components for biotechnological applications. The field includes engineering of proteins and nucleic acids by rational and combinatorial means for diagnostic, bioseparation and therapeutic applications, and involves both biological and synthetic production routes of biomolecules.

4.2 Present research topics Present research topics in Molecular Biotechnology includes the development and use of different platform technologies for analysis of biomolecule libraries, including several so called molecular display technologies. Special attention are directed to biomolecular interaction, involving studies and development of proteins/enzymes with desired recognition selectivity as well as novel biosensing principles. Applications of developed reagents and principles are broad and include for example bioseparation, cell biology, in vitro diagnostics, in vivo diagnostics/imaging and therapy. 4.3 Structure of the education The education in Molecular Biotechnology at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Molecular Biotechnology. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 4.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In the case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 4.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 4.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level.


11

Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the specialization area Molecular Biotechnology students need to have acquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - BB1030 Microbiology - BB1110 Gene Technology and Molecular Biology - BB1130 Analysis and Purification of Biomolecules These so called special admission requirements concerning courses or oher qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 4.5 Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),


- DOCTORAL THESIS -




• For any paper included his/her contribution should be significant and clearly identifiable.


12

• The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least one senior scientist.













by at least two senior scientists and the director of postgraduate studies. 5. Specialization Area of Glycoscience 5.1 Description of the specialization area The fundamental knowledge on cell wall polysaccharide biosynthesis, self-assembly and remodeling is exploited in multidisciplinary approaches to engineer novel biomaterials with high performance relevant to a wide range of industries. In addition, the knowledge gained from the characterization of the enzymes involved in cell wall formation is exploited for the


13

control of diseases caused by microbial pathogens and to characterize the mode of action of novel environmentally-friendly growth inhibitors targeted to cell wall biosynthesis (e.g. herbicides, fungicides, etc). 5.2 Present research topics Research and postgraduate studies in Glycoscience include enzymatic or microbial production, degradation or modification of natural fiber materials such as cellulose, and hemicelluloses. The research is focused in various areas of glycoscience, comprising fundamental research on plants and microorganisms, as well as biotechnological developments towards carbohydrate-based/related products. A major goal is to understand how extracellular polysaccharides in microorganisms and plants - especially trees - are formed, remodeled and hydrolyzed, and to exploit this knowledge toward a wide range of applications relevant to multiple sectors including (but not limited to) the forest industry (development of novel pulp and paper processes, of nanocomposites and biomimetic materials with a high-added value, etc), the biomedical industry (e.g engineering of carbohydrate-based wound-healing products), the agriculture industry (e.g. development of approaches for biofuel production, for crop protection), and the aquaculture industry (e.g. development of control measures of microbial diseases for optimization of food production). 5.3 Structure of the education The education in Glycoscience at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Glycoscience. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 5.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 5.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 5.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level.


14

Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligible for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the specialization area Glycoscience students need to have acquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - BB1080 Biochemistry, theory - BB2420 Glycobiology and Carbohydrate Technology - BB2450 The Cell Factory These so called special admission requirements concerning courses or other qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 5.5 Thesis The thesis part is an obligatory part of the research education. In addition to the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),


- DOCTORAL THESIS -




• For any paper included, his/her contribution should be significant and clearly identifiable.


15

• The thesis shall be pre-examined prior to printing, in addition to the main supervisor, also by at least one senior scientist.



should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor, also





• The student should appear as first author on at least one of the papers included. • For any paper included, his/her contribution should be significant and clearly identifiable. • If the thesis includes one or more paper which are published or formally accepted for




should be publishable in international peer-reviewed scientific journals. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor, also


6. Specialization Area of Gene Technology 6.1 Description of the specialization area Research and postgraduate studies in Gene Technology include both methodological and biological aspects concerning focused or genome wide studies of transcriptomes, genomes and epigenomes, including both quantitative and qualitative questions.


16

6.2 Present research topics Present research topics in Gene Technology includes methodology development concerning large-scale parallel nucleic acid sequencing and analysis, related to biological interrogations of widely different topics, including for example cancer origin and development, RNA silencing, stem cell differentiation, genetic variation, alternative splicing, tree genetics and animal domestication. 6.3 Structure of the education The education in Gene Technology at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Gene Technology. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 6.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In the case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 6.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 6.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level. Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved.


17

Further, in order to be able to fully benefit from the research studies in the specialization area Gene Technology students need to have acquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - BB1030 Microbiology - BB1110 Gene Technology and Molecular Biology - BB1130 Analysis and Purification of Biomolecules These so called special admission requirements concerning courses or oher qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 6.5 Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),


- DOCTORAL THESIS -




• For any paper included, his/her contribution should be significant and clearly identifiable. • The thesis shall be pre-examined prior to printing, in addition to the main supervisor also




should be publishable in international peer-reviewed scientific journals.


18

• The thesis shall be pre-examined prior to printing, in addition to the main supervisor also by at least two senior scientists and the director of postgraduate studied.










7. Specialization Area of Bioinformatics and Systems Biology 7.1 Description of the specialization area Research and postgraduate studies in Bioinformatics and Systems Biology include the application of statistics and computer science to the field of biological sciences. Bioinformatics entails the creation and advancement of databases, algorithms, computational and statistical techniques and theory to solve formal and practical problems arising from the management and analysis of biological data. Systems biology is an inter-disciplinary study field that focuses on complex interactions in biological systems, using a holistic rather than reductive perspective. 7.2 Present research topics Present research topics in Bioinformatics and Systems Biology includes an immense effort to use experimental data and bioinformatics platforms to map all the individual proteins of the human proteome to their locations within cells, body fluids, tisues and organs. Special attention are directed to differences in abundance and location that could be signatures of disease and therefore of diagnostic and therapeutic relevance.


19

7.3 Structure of the education The education in Bioinformatics and Systems Biology at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Bioinformatics and Systems Biology. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 7.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 7.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 7.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level. Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the specialization area Bioinformatics and Systems Biology students need to have acquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - DD2397 Applied Bioinformatics


20

- B2XXX Proteomics - BB2440 Bioinformatics and Biostatistics These so called special admission requirements concerning courses or oher qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 7.5 Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),


- DOCTORAL THESIS -











Compiled thesis (sv. "sammanläggningsavhandling") • The thesis should normally be based on two papers.


21

• The included papers need not to be already published or formally accepted for publication ("in press") in peer-reviewed international scientific journals. However, at least one manuscript should normally be included as "submitted for publication" to an international peer-reviewed scientific journal.






by at least two senior scientists and the director of postgraduate studies. 8. Specialization Area of Nanobiotechnology 8.1 Description of the specialization area Research and postgraduate studies in Nanobiotechnology include development and studies of miniaturized systems for performing cell and biomolecular analyses and manipulations. 8.2 Present research topics Present research topics in Nanobiotechnology includes for example the development of platforms for rapid on-site analysis of the biomolecular content of complex samples and multiplexed array formats for analysis and regulation of cell growth. Special attention is directed to development of high throughput microdroplet formats for transport, compartmentalization, analysis and sorting of cells and and particles. 8.3 Structure of the education The education in Nanobiotechnology at research level comprises both a course part and a thesis part. Courses are categorized into advanced courses, research skill courses, broadening courses and other courses. Some courses are obligatory for the students within the specialization area of Nanobiotechnology. Courses can be arranged by the home university, or other national or international universities, institutes or companies (see section 8.4). Note that the quality and level of courses arranged by others than university bodies need to be approved by the director of post-graduate studies before these can be part of an individual course package. In the case a licentiate degree exam is not the goal, a "two-year-seminar" is recommended to be held after ca. 20-26 months of studies, at which the student describes the progress so far, incl. both courses and thesis work, as well as the plans forward. Two senior scientists are


22

appointed to give their feed back to the student and the main and co-supervisors. The thesis part of the education is based on an accumulation of own theoretical and/or experimental data in the field, leading to the completion of a written thesis which can be defended at a dissertation at the end of the studies (see section 8.5). The education is performed under guidance by a main supervisor, together with one or several co-supervisors, in accordance with an Individual Study Programme (ISP) updated at least annually and approved by the director of post-graduate studies. 8.4 Obligatory and recommended courses A licentiate degree exam comprises a course part corresponding to at least 30 ECTS credits and a thesis part of 90 ECTS, accumulating to at least 120 ECTS credits of studies (i.e corresponding to two years of full-time studies). At least 50 % of the course credits should correspond to courses at research level. A doctoral degree exam comprises a course part corresponding to at least 60 ECTS credits and a thesis part of 180 ECTS, accumulating to at least 240 ECTS credits of studies (i.e corresponding to four years of full-time studies). At least 60 % of the course credits should correspond to courses at research level. Obligatory and recommended courses Lista över obligatoriska/rekommenderade kurser för lic och dok, i enlighet med tabell i bilaga 3. Crediting of earlier taken courses In some cases, courses taken before admittance to research education at KTH can be credited, after approval by the main supervisor and consultation of KTH general regulations concerning the crediting of earlier taken courses. Note that 60 % of the 60 ECTS course credits required for a doctoral exam need to correspond to courses at research level. For basic level educations eligibile for admission to research studies and comprising up to 240 ECTS, no crediting of courses from the basic education can be approved. Further, in order to be able to fully benefit from the research studies in the specialization area Nanobiotechnology students need to have aquired a deepened knowledge in the subject corresponding to or being equivalent to the following courses at KTH: - BB1110 Gene Technology and Molecular Biology - BB1130 Analysis and Purification of Biomolecules - BB2XXX Nanobiotechnology These so called special admission requirements concerning courses or oher qualifications needed to benefit from the research education, means that such courses or corresponding ones can not be credited in the individual course package of 60 ECTS. 8.5 Thesis The thesis part is an obligatory part of the research education. In addition the the general thesis quality assessment routines at KTH, (http://intra.kth.se/regelverk/utbildning-forskning/forskarutbildning/disputation/policy-for-forhandsgranskning-av-doktorsavhandling-licentiatuppsats-1.27246),


23


- DOCTORAL THESIS -
















24





9. Eligibility and Selection

9.1. Basic and special eligibility and prior knowledge

Eligibility to the Doctoral Programme in Biotechnology first involves the basic requirements for admission to research studies in general set forth by the Swedish Government (see "Högskoleförordningen", chapter 7, §39):

1. a completed university exam at advanced level,

2. fullfilled course requirements of at least 240 ECTS, of which at least 60 ECTS is at advanced level, or

3. corresponding merits acquired through other procedures

Further, for admission to the Doctoral Programme in Biotechnology, the completed university exam or the advanced level courses should be in the subject area of biological life science or biotechnology. In addition to these requirements, also special requirements for a particular specialization area may apply. These are in such cases described in the section "Crediting of earlier taken courses" for each respective specialization area. When included, these requirements are deemed necessary for the students to profit from the training, and may for example involve knowledge/skills from university studies in particular areas of importance for the subject area or language skills. The requirements are the same for students aiming for either doctoral or licentiate degrees.

9.2 Selection criteria

The selection of students to research education is first based on that they formally fulfill the admission criteria. In addition, their ability to fully benefit from the research education is assessed during the admission process, typically through interviews and reviewing earlier activities, exams and records, but also through an evaluation of the talent, degree of maturity, independency, expression ability in writing and speech, language skills and ability of critical thinking. The selection is done by the Dean of the School of Biotechnology after assessment of the appointed main supervisor and co-supervisor(s) by the Director of postgraduate studies


25

.

10. Examina and Tests in the Education

10.1 Licentiat and doctoral exams Licentiate and doctoral degree exams are performed according to the KTH regulations (see "KTH-handboken" at http//:intra.kth.se). A licentiate degree exam may be a final exam. Even if a doctoral exam is the final exam, a licentiate degree exam may first be taken. Briefly, in addition to completion of full course packages of 30 or 60 ECTS, for licentiate and doctoral degree exams, respectively, both exams involve a defence of a thesis as a result of theoretical and/or practical investigations. A licentiate thesis is presented at a public seminar. The licentiate theis shall be examined by at least one lecturer/senior scientist. The main supervisor decides on pass or not. A doctoral thesis exam involves a public defence seminar at which the thesis is examined by an opponent and an evaluation committe consisting of three or five members, the latter deciding on approval of the thesis or not. 10.2 Tests that are included in the education Courses in the research education shall preferably involve either an oral or written examination. The examinor must in each individual case ascertain that the student has fullfilled the course requirements.

APPENDIX 2: Listing of supervisor capacity

DOCTORAL PROGRAMME IN BIOTECHNOLOGY APPENDIX 2

Listing of supervisor capacity

At present, more than 20 senior scientists at the School of Biotechnology comply with the formal requirements to act as main supervisors; i.e. holding at least a 50 % full-time permanent employment at KTH and with academic merit levels of associate professor (docent) or higher. Further, a number of PhDs are active at the BIO School as senior scientists and some of them are likely promoted to associate professors within 5-10 years, and thus can act as main supervisors for licentiate or doctoral degree students. It can be estimated that three of the presently active eleven professors are retiring from their positions in the coming ten-year period (2011-2020). Below, the existing and some future potential supervisors are listed, including their main areas of expertise in relation to the seven specialization areas of the doctoral programme in Biotechnology. BIO

PROCESS ENGINEERING

BIO CHEM

MOL BIO

GLYCO SCIENCE

GENE TECH

BIOINF SYSTEM BIOL

NANO BIO

Professors Mathias Uhlén Gen Larsson Vincent Bulone Helene Andersson-‐Svahn Stefan Ståhl Per-‐Åke Nygren Sophia Hober Joakim Lundeberg Pål Nyrén Per Berglund Karl Hult

Associate Professors Peter Nilsson Gunaratna Kuttuva Rjarao Harry Brumer Mats Martinelle Torbjörn Gräslund Amelie Eriksson-‐Karlström Andres Veide

2

Anna Olsson Ines Ezcurra Torkel Berglund Afshin Ahmadian Christina Divne Doctors/Senior scientists Peter Savolainen John Löfblom Patrik Samuelson Emma Lundberg Johan Rockberg Henrik Wernerus Jenny Ottosson Björn Renberg Veronique Chotteau Qi Zhou Henrik Aspeborg Tommy Nordström Olof Emanuelsson Anders Andersson Pelin Akan Ann-‐Charlotte Sonnhammer Patrik Ståhl

APPENDIX 3: Course list

DOCTORAL PROGRAMME IN BIOTECHNOLOGY APPENDIX 3

Course list Obligatory (O) and recommended (R) courses for the different specialization areas of the single research education subject Biotechnology within the Doctoral Programme of Biotechnology. The courses are divided into the four categories (A) Advanced courses, (B) Research skill courses, (C) Broadening courses, and (D) Other courses. Advanced Courses

Staus of course in each Specialization Area: Obligatory (O); Recommended (R)

Code

Name of course Credits (ECTS)

BIO CHEM

BIO PROCESS

ENG

MOL BIO

TECH

GLYCO SCIENCE

GENE TECH

BIOINF SYSTEM

BIOL

NANO BIO

3A5102 Allmän biokemi (revidering poäng) 15 (12) R 3A5202 Animalcellteknologi 6.0 O BB3100 Biofiberresurser 4.5 R 3A5104 Biokemi (revidering poäng) 7.5 (6.0) R 3A5315 Biokemisk analys och

separationsteknik 7.5 O R R R

3A5204 Bioprocessteknik 6.0 R 3A5601 Bioteknik för massa- och

papperindustrin 6.0 R

BB3010 Bioteknik för massa- och papperindustrin

6.0 R

TBD Flow cytometry course R R KTH Physics

Microscopy course R R R

3A5108 Enzymkatalys 7.5 O 3A5209 Litteraturkurs i bioprocessteknik 7.5 O (1) BB3110 Python för beräkningsvetenskaper 5.0 R 3A5207 Uppskalning av fermentations-

process 4.5 R

Sthlm Univ.

Immunology 15 R R R

BB3020 Biomimetisk fiberteknologi 5.0 O TBD Biotechnology, reading course

(specialization area specific topic) 15 O O O O O O

BB2010 Environmental toxicology 9.0 R R R R R R R 15.0

ECTS as O

21.0 ECTS as O

15.0 ECTS as O

27.5 ECTS as O

15.0 ECTS as O

15.0 ECTS as O

15.0 ECTS as O

(1) Not obligatory for Licentiate degree students

For doctoral degree students within the specialization areas Biochemistry, Molecular Biotechnology, Gene Technology, Glycoscience, Bioinformatics and Systems Biology, and Nanotechnology, the course "#TBD Biotechnology, reading course" is obligatory. This course is preferably taken during year three or four, and serves as a deepening course in a subject of central importance for the students project(s). Research Skill Courses


Code


BIO CHEM

BIO PROCESS

ENG

MOL BIO

GLYCO SCIENCE

GENE TECH

BIOINF SYSTEM

BIOL

NANO BIO

1N5113 Theory of Science and Research Method, Technol. and Nat. Sciences

7.5 O O O O O O O

7.5 ECTS as O

7.5 ECTS as O

7.5 ECTS as O

7.5 ECTS as O

7.5 ECTS as O

7.5 ECTS as O

7.5 ECTS as O

2

If not already taken before admission to research studies (for example the KTH D-level course "AK2036 Scientific Theory and Research Methodology", obligatory for KTH Master students in Medical Biotechnology or Environmental and Industrial Biotechnology), a course in research methodology is conditionally obligatory for all students of the Doctoral Programme. The KTH course "1N5113 Theory of Science and Research Method, Technological and Natural Sciences" is listed here as a course on this theme, but this particular course may be exchanged for an equivalent one.

Broadening Courses


Code


BIO CHEM

BIO PROCESS

ENG

MOL BIO

GLYCO SCIENCE

GENE TECH

BIOINF SYSTEM

BIOL

NANO BIO

TBD Aktuella frågeställningar inom biokemi 1

3.0 R


3.0 R


3.0 R


3.0 R

TBD Current trends in high throughput biology 1

O


R


R


R

3A5320 Aktuella frågeställningar inom molekylär bioteknologi 1

3.0 O O O


3.0 R R R


3.0 R R R


3.0 R R R

TBD Aktuella frågeställningar inom glykovetenskap 1

3.0 O


3.0 R


3.0 R


3.0 R

TBD Aktuella frågeställningar inom bioprocessteknologi 1

3.0 O


3.0 R


3.0 R


3.0 R

0.0 ECTS as O

3.0 ECTS as O

3.0 ECTS as O

3.0 ECTS as O

3.0 ECTS as O

3.0 ECTS as O

3.0 ECTS as O

The courses listed here are annually arranged literature seminar courses, in which research topics of general and broad interest are presented and discussed. The courses serve as an important forum for cross-disciplinary interactions, scientific and social networking and competence broadening. For the indicated specialization areas, it is obligatory or recommended to participate in at least one full-year round of these seminar series for both doctoral and licentiate degree students.

Other Courses


Code


BIO CHEM

BIO PROCESS

ENG

MOL BIO

GLYCO SCIENCE

GENE TECH

BIOINF SYSTEM

BIOL

NANO BIO

3A5311 Aktuella frågeställningar inom biovetenskap 1

3.0 O


3.0 R

3


3.0 R


3.0 R

TBD Aktuella frågeställningar inom bioinformatik and systembiologi 1

O


R


R


R

3A5316 Aktuella frågeställningar inom DNA/RNA-vetenskap 1

3.0 O


3.0 R


3.0 R


3.0 R

TBD Aktuella frågeställningar inom protein och enzymvetenskap 1

3.0 R O


3.0 R R


3.0 R R


3.0 R R

LH200V Basic communication and teaching (GKU)

3.0 O O O O O O O

3A5801 Aktuella frågor inom nanobioteknik 3.0 O BB3120 Handledningsmetodik flör

projektarbete 6.0 R R R R R R R

BB3090 Intoduktion till Biomime och dess forskning

1.5 R

3.0 ECTS as O

3.0 ECTS as O

6.0 ECTS as O

6.0 ECTS as O

6.0 ECTS as O

6.0 ECTS as O

6.0 ECTS as O

The courses 3A5311-3A5314 correspond to annually arranged seminar series within protein science, and the participation in at least one full-year seminar round is obligatory for both doctoral and licentiate degree students within the specialization area Molecular Biotechnology. Likewise, the courses 3A5316+3A5324-3A5326 correspond to seminar series in the field of nucleic acid technologies, and at least one full-year round of seminar series is obligatory for both doctoral and licentiate degree students within the specialization area Gene technology. The courses #XXX-XXX "Aktuella frågeställningar inom protein och enzymvetenskap" (3.0 ECTS) correspond to annually arranged seminar series within protein and enzyme science, and the participation in at least one full-year seminar round is obligatory for both doctoral and licentiate degree students within the specialization area Glycoscience (recommened course for the specialization area Biochemistry). For both doctoral and licentiate degree students within the specialization area Bioinformatics and System Biology, at least one full-year round of the seminar series #TBD "Bioinformatik and Systembiologi" (3.0 ECTS) is obligatory. For both doctoral and licentiate degree students within the specialization area Nanobiotechnology, the participation in one full-year round of a seminar series in the course #3A5801 " Aktuella frågor inom nanobioteknik" (3.0 ECTS) is obligatory. The course "LHV200V Basic Communication and Teaching" (or an equivalent course) is obligatory for research students in all specialization areas which will act as teachers or laboratory assistants during their research studies. It is thus considered conditionally obligatory for the Doctoral Programme in Biotechnology.

Summary of obligatory and conditionally obligatory course credits per specialization area BIO

CHEM BIO

PROCESS ENG

MOL BIO

GLYCO SCIENCE

GENE TECH

BIOINF SYSTEM

BIOL

NANO BIO

Obligatory 15.0 24.0 21.0 33.5 21.0 21.0 21.0 Conditionally

Obligatory 10.5 10.5 10.5 10.5 10.5 10.5 10.5

4

Total 25.5 ECTS

34.5 ECTS 31.5 ECTS 44.0 ECTS

31.5 ECTS

31.5 ECTS 31.5 ECTS

The total number of obligatory credits varies between 25.5 and 31.5, depending on specialization area. This corresponds to 42.5 to 52.5 % of the 60 ECTS of courses required for a doctoral degree exam.

APPENDIX 4: Listing of national and international networks

DOCTORAL PROGRAMME IN BIOTECHNOLOGY

APPENDIX 4

Listing of national and international networks related to the doctoral

programme in Biotechnology (as of autumn 2010)

Name Type of Network

Host /coord. body

Main Financial Support

Approx. Duration

ProNova VINN Excellence Centre for Protein Technology

Industry/academia collaboration center

KTH VINNOVA 2017

BIOMIME Strategic competence center

KTH SSF 2012

AFFINOMICS EU consortium Uppsala University

EU 2015

FLUODIAMON EU consortium KTH EU 2012 SAPRO

EU Initial Training Network

Univ. of Aberdeen

EU 2013

RENEWALL EU consortium Univ. of York EU 2012 ARC Centre for Plant Cell Wall Biology

Academia/industry centre of excellence

Univ. of Adelaide Australian Research Council

2018

Working on Walls

International graduate training network

Univ of British Columbia

NSERC

2014

Biomime Graduate Research School

Research School KTH Formas 2013

CarboMat

Research Centre (“Strong Research Environment”)

KTH Formas 2015

Hiperdarp EU consortium MS Italy EU 2012 CASCAT COST Action EU 2013 BIO-‐AMINES Industry/academia

research project KTH VINNOVA 2013

MIRACLE EU consortium IMAC EU 2014 DIGITAL SEQUENCING

EU consortium Ling Vitae EU 2014

CHEMORES EU consortium Karolinska Institute

EU 2012

SNISS RFI Infrastructure KTH VR 2014 SciLifeLab Strategic center KTH VR 2014

Documents

Applicationfor!a! Doctoral!Programme!in!Biotechnology!/Bioteknologi (V...2 . 1. Programme Name . Eng: Doctoral Programme in Biotechnology Swe: Doktorsprogram i Bioteknologi . 2. Scientific