Introduction to Systems Biology 2012-2013
Students for Systems biology in Practice: see Systems Biology in Practice
Welcome to the wiki of Introduction to Systems Biology 2012-2013
for students from last year, see: Introduction to Systems Biology 2011-2012
General information about the course can be found in this document: Media:general information introSB 2012-2013.pdf
- please read this carefully!!
The schedule of the course and important dates for the course can be found in this document:
Media:Planning_IntroSB_2012_2013.pdf Please note that this schedule is still somewhat flexible and may change, but not the locations and times.
Literature assignment information and groups Media:Topics literature study 2012-2013_groups_assigned.pdf
Do not hesitate to contact your supervisor!
Example of an abstract
Here is an example of an abstract. It discusses a subject, its status quo, and places a few recent scientific papers in this context. Not a thorough scientific review, but food for thought for the general scientific reader. Who should pay for the police?
Your final grade for Introduction to Systems Biology will consist of the following components:
- 30% deficiency courses (all deficiencies having equal weight)
- 40% assignments (all assignments having equal weight)
- 15% individual abstract about the literature subject
- 15% group presentation about the literature subject
mail to firstname.lastname@example.org
mail to email@example.com
- assignment: Media:Metabolic reconstructions_2012-2013.pdf
mail to firstname.lastname@example.org
September 13th: first Artis lecture!
Lecture series of Microbial Genomics in Artis are on September, 13, 20 and 27. Coordinator is prof Remco Kort (email@example.com).
Please find the following information below:
- The lectures will take place in Artis Zoo, in the lecture room “De Volharding” (map number 42 Media:Artismap.pdf), which is situated at 10-15 min. walking distance from the main entrance.
- On the first day on September the 13th, from 9.25 A.M., you will receive your entrance tickets for all 3 lectures (and October 26 for the SB students) , which will give access to Artis on the lecture dates
- Be aware that the lectures will start 10.00 A.M. sharp, and there will be no entrance to the lecture room after 10.00 A.M. Lectures will end at 12.00 A.M. (coffee break from 11.00 to 11.15 A.M.)
Please take notice of the following regulations:
- The lectures are obligatory for VU students
- Students need to register for each lecture by their signature before entrance of the lecture room
- It is not allowed to eat or drink in the lecture room
- Switch off mobile phones, i-pods, etc.
- assignment: Media:Assignment JWS online_2012_2013.pdf
mail to firstname.lastname@example.org
September 20th Lectures in Artis
Math test: time: 15.30 - 17.30 locations are : C659 for last name until M M212 for last name from N
- Slides of the lecture by Dr. Hoefsloot: Media:Top_Down_Sysbio.pdf
Additional information can be found in the following three papers
When working from your own PC, see the library website how to get access to online journals (Menu point "Facilities: Working from home").
Mathematica Exercises can be found here: http://wiki.cs.vu.nl/mp/images/9/9d/Mathematica_lecture.zip Answers can be found here: http://wiki.cs.vu.nl/mp/images/4/46/Mathematica_lecture_answers.zip
Also, VU students can download Mathematica for free at: http://www.nat.vu.nl/~ivo/MM/MM8.04 To activate your copy of Mathematica, please visit: http://itg.few.vu.nl/applications/303/Mathematica_site_license.html
- Slides of the lecture by Prof. Teixeira de Mattos: Media:Intro_SysBiol_okt_2012.pdf
- Description: Media:Assignment_balances.pdf
- Excel file: Media:micfyscalcexercise.xls
- Papers: Bekker et al 2009 and Sharma et al. 2012
Note: updated Excel file Media:micfyscalcexercise_v2.xls
- Lecture notes by Prof. Bruggeman Media:handout_signaling.pdf
- Assignment signalling (Mathematica file) Media:Signalling_exercises.zip
- Lecture notes trade-offs by Prof. Bruggeman media:handout_trade_off_cost_benefit.pdf
- Assignment trade-offs (Mathematica file) media:trade_off_optimization_exercises.zip
- Lecture notes low molecule numbers by Prof. Bruggeman media:handout_low_molecule_number_biology.pdf
Announcement: Systems Biology in Practice
Welcome to Systems Biology in Practice. We will start on Monday, october 29 and I beg you ALL to convene this Monday at 9.00 am at the Science Park in Room G5.29. I will there and then explain the set-up of the course and present the complete and final programme with all info you need. For now, I attach the provisional scheme (which is close to the final one but still lacks some room numbers). Subsequently, the lecture on Microbial Physiology will start
Please be there!! I would like to receive a confirmation that you have received this email
See you all on Monday, october 29, at 9.00 am in room G5.29 at the Science Park
Joost Teixeira de Mattos