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IST Core Course

Instructors: Nick Barton, Gaia Novarino et al.

Teaching Assistants: Christoph Dotter, Fabienne Jesse, Alexandr Kazda, Sebastian Novak, Barbora Trubenova,

Description

The IST Core Course is the ISTScholar PhD Program's signature interdisciplinary course, required for all students of each year's cohort. It is scheduled for a full semester and awards 6 ECTS credits. Students will work together in teams to solve various tasks that highlight different aspects of a central theme, and that give them the opportunity to develop creative approaches to fundamental problems.

Course format

The course includes lectures, group discussion, supervised group-work, presentations, and feedback sessions. Lectures and recitations will be arranged to match these diverse formats, generally without distinguishing between the two. Active participation is required from students.

Goals of the course

The goals of the IST Core Course are to encourage interdisciplinary research, and more broadly, to foster a set of skills that are valuable in- and outside of academia. To do so, the course focuses on the following:

Non-goals of the course

It should be stressed that the IST Core Course does not aim to teach specific in-depth skills in any particular discipline (like programming, sequencing, equation solving, etc.). In particular, the scientific theme of the course is meant to serve as a vehicle for achieving the above goals.

Role of teaching assistants

The teaching assistants for this course have different areas of expertise and will be able to help you with different (parts of) the assignments. Individual assignments will specify the responsible or most relevant TAs and potential external helpers, but students and student teams are free to approach all of the TAs with their questions.

In addition, each student team will be assigned a specific TA who will serve as their "course mentor". This is the person they should turn to if they are generally stuck or don't know who to turn to, if there are unsolvable issues within the group, or for any administrative issues relating to the course.

 

Requirements, grading, and feedback

Students will be graded on a pass/fail basis, yet will receive feedback about their performance throughout the course. Student evaluation is based on individual and group performance, which will be assessed in three categories: submission and defense of a final project, completion of homework assignments, and active classroom participation. Each of these categories have to be passed individually.

Classroom participation

Students are expected to attend all classes. Unavoidable absences should be communicated to the TAs. During class, students are required to contribute to discussions and highly encouraged to ask questions.

Assignments

A series of homework assignments will provide the basis for the final project at the end of the course. Assignments typically consist of a team phase and an individual phase:

For each assignment, a discussion date and a due date will be specified. The individual write-ups should be submitted in electronic form to corecoursetas@ist.ac.at as specified on each assignment.

Final project

Towards the end of the course, each team will collaborate on a final project that subsumes and extends the material covered in class and in the assignments. Each team submits a paper write-up and defends its project in front of an audience. The exact scope of the project is defined by each team individually, and guidance according content and length will be given. For time reasons, the projects will be presented and defended on January 31st and February 2nd, i. e. after the Institute's exam week.

Schedule (subject to change)

Date Time Topic Location Other
Tuesday, October 18th 8:45-10:00 Overview / Introduction Big Seminar Room Lab Building West (GF) Syllabus slides
Thursday, October 20th 8:45-10:00, 10:15-11:05 Discussion:Modelling in different fields Big Seminar Room Lab Building West (GF) interesting Article
Tuesday, October 25th 8:45-10:00 Autism: The problem Big Seminar Room Lab Building West (GF) Lecture Slides
Thursday, October 27th 8:45-10:00, 10:15-11:05 Discussion: How to address the problem Big Seminar Room Lab Building West (GF) Lecture Slides and Web Reference
Tuesday, November 1st       Public holiday - no class
Thursday, November 3rd 8:45-10:00, 10:15-11:05 Lab work in groups Big Seminar Room Lab Building West (GF) / Labs (tbd) may extend to Friday, November 4th (details tbd)
Tuesday, November 8th 8:45-10:00 Summary/recap of lab work Mondi 2 Lecture Slides
Thursday, November 10th 8:45-10:00, 10:15-11:05 Lab work: group exercise Lake View Room (Restaurant 1st floor)  
Tuesday, November 15th 8:45-10:00 Alignment: group exercise Big Seminar Room Lab Building West (GF)  
Thursday, November 17th 8:45-10:00, 10:15-11:05 Alignment and data Big Seminar Room Lab Building West (GF) Mathematica file and Data file
Tuesday, November 22nd 8:45-10:00 Guest Lecture: Algorithms Big Seminar Room Lab Building West (GF) Lecture handout
Thursday, November 24th 8:45-10:00, 10:15-11:05 Statistical inference Big Seminar Room Lab Building West (GF) Gambling widget, the Ioannidis paper, and a video
Tuesday, November 29th 10:15-11:30 Statistical inference Big Seminar Room Lab Building West (GF) Lecture notes, Papers on climate change, and a note on the Ioannidis discussion
Thursday, December 1st 8:45-10:00, 10:15-11:05 Do gene expression patterns differ? Big Seminar Room Lab Building West (GF) Gene expression notebook
Tuesday, December 6th 8:45-10:00 Do gene expression patterns differ? Big Seminar Room Lab Building West (GF)  
Thursday, December 8th       Public holiday - no class
Tuesday, December 13th 8:45-10:00 Networks: protein-protein, co-expression Big Seminar Room Lab Building West (GF) Lecture slides
Thursday, December 15th 8:45-10:00, 10:15-11:05 Recap & project brainstorming Big Seminar Room Lab Building West (GF)  
Tuesday, December 20th 8:45-10:00 Guest lecture: Networks Big Seminar Room Lab Building West (GF) Lecture slides and Mathematica tools
Thursday, December 22nd 8:45-10:00, 10:15-11:05 Guest lecture: Clustering and project feedback session Big Seminar Room Lab Building West (GF) Lecture slides
Tuesday, January 10th 8:45-10:00 Some evolutionary approaches to understanding disease Big Seminar Room Lab Building West (GF) Lecture slides
Thursday, January 12th 8:45-10:00, 10:15-11:05 Group work on project Big Seminar Room Lab Building West (GF)  
Tuesday, January 17th 8:45-10:00 Group work on project Big Seminar Room Lab Building West (GF)  
Thursday, January 19th 8:45-10:00, 10:15-11:05 Group work on project Big Seminar Room Lab Building West (GF)  
Tuesday, January 24th 8:45-10:00 Guest lecture: Systems biology Big Seminar Room Lab Building West (GF)  
Thursday, January 26th 8:45-10:00, 10:15-11:05 Group work on project / Wrap-up Big Seminar Room Lab Building West (GF)  
Tuesday, January 31th 8:45-10:00 Final presentations Big Seminar Room Lab Building West (GF)  
Thursday, February 2nd 8:45-10:00, 10:15-11:05 Final presentations Big Seminar Room Lab Building West (GF)  

Assignments

File Due Date Comments
Assignment 0 Oct 25  
Assignment 1 Nov 8 Forum for questions
Assignment 2 Nov 17  
Assignment 3 Nov 22  
Discussion questions Nov 29 No written assignment, discussion only!
Assignment 4 December 13 Lecture notebook (from Dec 1) and key results (contains optional code)
Final Project see prompt some databases (more upon request!)

Reading material for Assignment 0

  Main Reference Extra material
Hodgkin-Huxley (up until approx Section 3.3) (original paper) Mathematica to play with
Turing (esp Sect 1-4 and 11)   Mathematica to play with
Polymer chains (Review paper)    
IS-LM (Review paper) (Chapters 2 and 5)  

References

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