Computational and Quantitative Biology PhD

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    Organization

     

    Objectives

    Computational Biology is a novel emerging discipline at the forefront of Computer Science, Physics, Engineering and Biology aimed at posing the main open questions for the understanding of the molecular basis of life as diseases in algorithmic terms. This involves the modeling of biological systems as sets of interacting entities and the definition of integration strategies from multiple sources of information to obtain more comprehensive models. Given the complexity of the underlying phenomena and the huge amount of data currently generated by modern “omics” technologies, Computational and Quantitative Biology are the ideal arena to develop and apply novel state-of-the-art machine learning models, exploratory algorithms for big data and computational statistics methodologies together with advances Systems Biology approaches in order to drive the next discoveries in the Life Science.

    The main objective of the Computational Biology PhD joint program is to train the next generation of scientists who are both passionate about developing novel computational strategies for molecular biology and are committed to functioning at a high level in both computational and biological fields. The program emphasizes multidisciplinary competency, interdisciplinary collaboration, and transdisciplinary research, and offers an integrated and customizable curriculum that consists of two semesters of formal teaching courses and experimental work tailored to each student’s background and interests, research rotations with faculty mentors spanning computational biology’s core disciplines, and dissertation research.

     

    Organization

    The CQB PhD program is subject to the University Doctoral Regulation. It is administratively managed by the Department of Electrical Engineering and Information Technologies (DIETI). It is accredited by the National Agency for Evaluation of Universities and Research (ANVUR).

    The duration of the PhD program is three years.

    Admission is based on a selection process, through an annual open call. Admission to the doctorate involves an exclusive and full-time commitment. A number of positions are reserved for applicants from abroad. An International Welcome Desk service is provided by the University to assist admitted foreign students. 

    The starting date of every academic year is November 1st.

    Every student is assigned by the Faculty Board  a supervisor (or tutor), and optionally a co-supervisor (or co-tutor). Students may be assigned a co-tutor from the external entity too, in case of research themes/scholarships funded by companies or external public or private research institutions.

    Bimonthly periodic reports need to be approved by the PhD Coordinator. 

    By the end of every academic year, on the basis of a detailed report of the individual activities and research, the CQB Faculty Committee  decides the admission of the student to the subsequent year, or proposes to the Magnificent Rector the exclusion of the student from the program. 

    At the end of the three-years program, the student has to present to the CQB Faculty Committee a detailed report of personal activities and of (co-)authored publications.

    Students will gain the Philosophiæ Doctor title (“Dott.Ric.” or “Ph.D.”) upon successfully passing a final exam (“thesis defense”), after the duration of the program. The final exam encompasses the evaluation of an individual doctoral research thesis contributing to the advancement of knowledge or methodologies in the selected field. The doctoral thesis is evaluated before the defense by at least two highly qualified professors (“thesis evaluators”) - possibly belonging to foreign institutions - different from those who contribute to granting the Ph.D. title. The Ph.D. title is granted by the Magnificent Rector of the Federico II University of Naples.

     

    Activity plan

    The activity plan is individual: every student shall determine with the supervisor(s) the educational activities to be periodically reported in the personalized study plan.

    Individual activity plans of students have to encompass an overall number of at least 180 credits within the duration of the program. 

    The CQB PhD study plan envisages three kinds of activities, which all need to be encompassed in individual study plans (according to the rules set below):

    • Courses / PhD Schools;
    • Seminars / Tutorials;
    • Research

    Every PhD student is expected to spend a study and research period between 3 and 18 (even not continuous) months in an internationally recognized academic or research hosting institution abroad. Activities abroad need to be approved by the CQB Faculty Committee in advance.

    All the above activities shall entitle students to earn corresponding educational credits.

    The number of credits for courses and PhD schools is typically defined by the PhD Board, depending on their duration, level and final assessment. Credits are gained upon successful course completion, as attested by the lecturer, typically on the basis of the final assessment.

    The number of credits for seminars is typically 0.2 credits per hour. Students may also earn credits attending tutorials at international conferences. Credits are gained upon successful attendance, as attested by the lecturer or by the Coordinator.

    The number of credits for individual research activities is attested by the student supervisor. Research activities include all kinds of not ex cathedra activities, such as: study of books and of the scientific literature; experimental and laboratory activities; attendance to scientific conferences and workshops and to technical meetings; participation to research projects meetings; talks, presentation and seminars; preparation of technical reports, of scientific articles and of the doctoral theses. Study and research periods abroad are included and shall be reported in the research activities.

    The organization of the educational activities in individual study plans is expected to adhere to the criteria for the number of yearly credits set in the following table, unless differently agreed with the PhD Board.

     

    Year

    Courses

    (credits)

    Seminars

    (credits)

    Research

    (credits)

    Tutorship

    (credits)

    I

    min 20 - max 40

    min 5 - max 10

    min 10 - max 35

    min 0 - max 1.6

    II

    min 10 - max 20

    min 5 - max 10

    min 30 - max 45

    min 0 - max 1.6

    III

    min 0 - max 10

    min 0 - max 10

    min 40 - max 60

    min 0 - max 1.6

    TOTAL

    min 30 - max 70

    min 10 - max 30

    min 80 - max 140

    min 0 - max 4.8

     

    The range of yearly credits per kind of activity is driven by the following criteria:

    • Attendance to advanced or interdisciplinary courses is expected to be favored in the first half of the duration of the PhD program, with the goal for the student of broadening personal knowledge in areas not covered in own prior MSc career. The categorization of courses is described below;
    • In the second year, the individual activity plan is expected to favor deepening knowledge in disciplines related to personal research interests; research activities in the second year start to become prevalent;
    • The student is also expected - mainly in the first two years - to attend ad hoc courses for stenghtening personal language and computer skills useful for research activities, and courses about research and innovation management and entrepreneurship;
    • Lab activities, attendance to conferences and seminars, and study and research periods abroad may take place during the whole PhD program duration;
    • In the third year, the student is expected to favor research activities in the scientific area of interest, which will result in the preparation of the doctoral research thesis.

    Throughout the whole CQB program, students may also earn from 0 to 4.8 credits (within the limit of 40 hours per academic year) for tutorship or supplementary teaching activities of undergraduate and graduate students. Tutorship duties are assigned by the coordinators of the undergraduate or graduate curricula under authorization of the ICQB Faculty Committee with the consent of the student, and need to refer to scientific disciplines characterizing the CQB program. Tutorship activities are attested by the CQB Coordinator.

    Courses are categorized in three types:

    1.  A) Advanced/interdisciplinary courses
      1.  A1) Ad hoc PhD courses (Core courses)
      2.  A2) Courses shared with MSc curricula (Elective courses)
    2.  B) English language, scientific writing, advanced computer skills courses
    3.  C) Ad hoc PhD courses on research enhancement, entrepreneurship and intellectual property 

    Type A1 courses are to be attended by all PhD students whose research area or interests (in a broad meaning) are related to the course topic.

    Type A2 courses may be freely selected by students, based on own past studies and on personal study and research interests, upon agreement with their PhD supervisor, with the goal of broadening and deepening personal knowledge and competences. Students may choose to attend other type A2 courses offered in MSc curricula of the Federico II University or of different universities, subject to prior approval by the PhD Board.

    Type B courses are mandatory; unattendance need to be justified to the Coordinator.

    Type C courses are mandatory; unattendance need to be justified to the Coordinator.

    Type A1, B and C courses are typically held every other year, allowing students to attend them in their three-years study plan.

    Individual study plans not adhering to the above rules need to be motivated and approved by the CQB  Board.

    Courses and seminars are listed in the related pages of the CQB web site.

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