Jon K. Lærdahl, Bioinformatics for Molecular Biology...MBV‐INF4410 –MSc level MBV‐INF9410...

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Jon K. Lærdahl,Structural Bioinformatics

Bioinformatics for Molecular BiologyMolecular Biology

MBV‐INF4410 – MSc level

MBV‐INF9410 – PhD level, version A

MBV‐INF9410A – PhD level, version B


Bioinformatics for Molecular Biology

C C di t D J K L d hl• Course Coordinator: Dr. Jon K. Lærdahl

• E‐mail: [email protected]

• Phone: +47 99 507 335

• Course wiki/web page:

h // iki i / j /MBV INFX410https://wiki.uio.no/projects/MBV‐INFX410

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Bioinformatics for Molecular Biology – 3 variants

Level Study points Exam Written assignment/assignment/essay

MBV‐INF4410 MSc 10 Yes Yes (at least1000 words)

MBV‐INF9410 PhD 10 Yes Yes (at least 1500 words)

MBV‐INF9410A PhD 8 Yes No

Home exam: • will be sent to all participants at 3 pm, Thursday December 6, by e‐mail•must be returned, at the latest, at 3 pm, Thursday December 13, by e‐mailEssay: • assignment must be returned by Monday, January 21, 2013, at 3 pm, by e‐mail


Bioinformatics for Molecular Biology

• Mainly intended for molecular biologists, biochemists and the like – for example with a Bachelor or MSc from the Department of Molecular Biosciences (IMBV)

• Also students with informatics and similar backgroundsimilar background

• Very demanding… Please, consider this when evaluating the course

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Jon K. Lærdahl,Structural BioinformaticsBioinformatics for Molecular

Biology – Goals• Get insight into the growing importance of informatics and

computations in biologyL t th UNIX d li d t b i f• Learn to use the UNIX command line and get a very brief taste of programming

• Learn how to obtain and work with data from biological databases

• Learn to find, install and run new bioinformatics tools and packages

• Learn to use some new tools, and to be critical about results

• Get an overview of some of the groups dealing with bioinformatics & computational biology in the Oslo region– Know were to go for help?

Jon K. Lærdahl,Structural BioinformaticsBioinformatics for Molecular

Biology – Goals

Understand a little bit more of this! • You should become more confident

Don’t panic if someone asks you to:• Find, install and run a program on your laptop• Download, install, run, and modify(?) a program on a Unix server•Make or modify a pipeline with several programs running one after the other

working on your own computer or a Unix server

• If you get help, for example setting up you computer on the UiO network, make sure you understand what was done!

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Bioinformatics for Molecular Biology – wiki

Structure of the course:• First basics, Unix, scripting, Python, R• Then more applications

https://wiki.uio.no/projects/MBV‐INFX410


Helpers for exercises/labs

Gro Nilsen Ksenia Khelik

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Your laptops• All students must bring a laptop

– Windows (Windows XP or more recent)– UNIX/Linux– UNIX/Linux– OS X (i.e. an Apple computer)

• The computer should not be more than 2‐3 years old • It should be possible to connect the computer to the UiO wireless

network • You must have a root/administrator password that gives you access

to installing new software on the computer • Bring an external mouse, and do not rely on touchpad/trackpadg y p p

only • You must

– have a valid UiO user account and must be able to log onto a computer on the UiO network

– or we will get you a UiO user account as soon as possible!

Jon K. Lærdahl,Structural BioinformaticsComputational resources

for this course You will do exercises both

• on your own laptop

• on the Unix serveron the Unix server freebee.abel.uio.no

Abel was (in June) 96 on the list of the most powerful computers in the world

258 TFLOP/s /theoretical peak performance

Freebee is a “small corner of Abel”

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Why not use the UiO computers?

Terminalstue/PC lab?

• This would certainly be easier...

• But, you would not easily get access to the resources after the course

• at home?• in your own lab?y• anywhere?


Exam

https://wiki.uio.no/projects/MBV‐INFX410#Exam

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Assignment (MBV‐INF4410/9410 only!)

https://wiki.uio.no/projects/MBV‐INFX410#Written_assignment


Calendar

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Details on all participants

• All students must send me an e‐mail with this content and format (to [email protected]):

“Course version” “e‐mail address” “full name”

I will send the exam and other information to this address

MBV‐INF9410A [email protected] Jon K. Lærdahl

for example, IMPORTANT!


Bioinformatics for Molecular Biology• Course Coordinator: Dr. Jon K. Lærdahl• Research Scientist

– Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology Rikshospitalet – Osloand Department of Microbiology, Rikshospitalet Oslo University Hospital (OUS)

– Bioinformatics Core Facility (CF), Department of Informatics, UiO

• Group: Torbjørn Rognes (http://www.ous‐research.no/rognes)

• Main research area: Structural and Applied Bioinformatics

• Background• Background– MSc (Trondheim): Organic Chemistry– PhD (Oslo) and PostDoc (Auckland, Oslo): Theoretical

Chemistry, Molecular Physics, Physical Organic Chemistry

– Last 10 years: Bioinformatics (UiO Biotech Centre & OUS)

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Computational Life Science (CLS) Centre

Ole‐Johan Dahls hus, 10. etasje –The hub for CLS and bioinformatics at the UiO


Computational Life Science (CLS) Centre

• All bioinformaticians and bioinformatics students from the Department of Informaticsfrom the epartment of Informatics

• Torbjørn Rognes group (my group)• CLSi ‐ an initiative from MLSUIO to develop and improve collaboration, research, services and education in the field of bioinformatics at the UiO

• Several people from medicine & USIT• Core Facility for Bioinformatics – help desk!• Room for guests!• Make sure you get a guided tour of the 10. etasjeduring the course!

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CLS Wednesday seminars –Bioinformatics/CLS seminars every 14 days


cbo‐[email protected] – the mailing list for bioinformatics and computational biology in the

Oslo region • News about • Seminars• Courses• Courses• Jobs• Conferences

Relevant mainly for people in the Oslo region

Anyone can send an e‐mail to the list

Curators check that the message is relevant (to avoid spam) and releases the message

Currently >330 subscribers

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First “tool” • Why not set up your own mailing list?

Jon K. Lærdahl,Structural Bioinformaticshttp://www.uio.no/tjenester/it

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What about those of you that are expert programmers and Unix users?

Come and talk to me in the first break!


We cannot lock the room during the breaks...

• Bring all valuables with us or something else?

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Any questions aboutAny questions about practical details?

Jon K. Lærdahl, Bioinformatics for Molecular Biology...MBV‐INF4410 –MSc level MBV‐INF9410...

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