Page AdvancedAlgorithms

This is the Wiki for a project-oriented version of P4.

Here you can find a StudentList

Direct links to topics

Algorithmic problems in RNA-Seq (1)

(Instructor team: Reinert, Weese, Andreotti, Holtgrewe, Kehr, mail: aa2010ss-rnaseq@lists.spline.de)

Algorithmic problems multiple genome comparison (2)

(Instructor team: Reinert, Andreotti, Holtgrewe, Kehr, mail: aa2010ss-GenComp@lists.spline.de)

Algorithmic problems in HPLC/MS based proteomics (3)

(Instructor team: Reinert, Andreotti, Bielow, Aiche, mail: aa2010SS-QuantProt@lists.spline.de)

Mail to all: aa2010ss-all@lists.spline.de Mail to instructors: aa2010ss-instructors@lists.spline.de

Exam results

If you want to have a look at your exam please come to the Sprechstunde. Here are the results of the second exam.

xxx6998	44	3.7
xxx8948	56	2.7
xxx8052	52	3.0
xxx7990	60	2.3
xxx4248	27	5.0
xxx9469	33	5.0

If you want to have a look at your exam please come to the Sprechstunde. A PDF with the correct solutions will be uploaded soon. I corrected the mark scale a bit in your favor.

xxx6998	25.5	5.0
xxx8948	33.5	5.0
xxx3310	37	5.0
xxx7891	46	3.3
xxx5340	44	3.7
xxx4016	46.5	3.3
xxx1420	56.5	2.3
xxx841	40	4.0
xxx7234	57	2.3
xxx7260	45.5	3.3
xxx8052	34	5.0
xxx3547	42	3.7
xxx5338	49.5	3.0
xxx7990	0	5.0
xxx9983	0	krank
xxx5740	0	5.0

Schedule

Here is the generic schedule which will be filled in as we go along. In any case the three core lectures will be given. Please note that ALL students should attend all lectures. Please update the schedule pages OFTEN!

Schedule for rehearsal and project presentation

We will have three presentation slots for the the three projects:

We have rooms: July 19th: 14-18, Room 006, T9 July 20th: 14-18, Room 049, T9 July 21st: 14-16, Room 031, A6

The rehearsals will be

• June 23rd: Genome Comparison 1, Proteomics 1
• June 30th: RNA-Seq 2, Genome Comparison 2
• July 5th: Proteomics 2, RNA-Seq 3
• July 7th: Proteomics 3
• July 9th: Genome Comparison 3

Tutorials

Corinna and Max will offer additional tutorials in preparation for the exam. The tutorials will be on Monday and Tuesday, July 19 and 20, and will each take about 3 hours (10 am to 1 pm). Contents will be RNA-Seq (Corinna) and Genome Comparison and Proteomics (Max).

Supplementary Pages

• Teaching
  The aggregated ideas that form the basis of how you might want to go about teaching your colleagues, and why.
• Presentations
  Some helpful hints on how to plan and deliver your presentations.
• Materials
  Texts, videos, and other suggestions for study regarding meta-skills.
• Forum
  For announcements, discussions, and questions that (potentially) concern everybody.

For materials on the writing and presentation components, see Peter Monnerjahn's Materials Page. He will be on hand in Session 3 each week to teach the writing and presentation skills required to earn credit for this module. For a group chat session, send an e-mail to make an appointment and visit my Office Hours page.

SVN access

I created a svn repository for each project. Please check out the directory with:

svn co https://svn.imp.fu-berlin.de/seqan/trunk/teaching/master/P4-2010

As with editing rights for the wiki, I need your FB username (if you click the link you can browse the repository).

Initial setup and Guidelines for lectures

Here you find the initial setup of the lecture.

After having finished the first week I can give you some guidelines about what to do when. Note: From June 2nd on we will swtich the role of Wednesday and Friday. That means the reiteration of the lecture and exercises will take place on Friday.

For the team preparing the next Monday lecture:

• Make an appointment with the instructor team to talk about a first version of the lecture. Be prepared by
  • having carefully read the literature
  • having noted down questions
  • Having a proposal of what to present and how At the end of the first meeting we will have one possible roadmap for the lecture which you can improve or change until Wednesday.
• Check in a first complete version of the lecture BEFORE the Wednesday lecture, so we can discuss it on then.
• During the monday lecture somebody takes notes about what to improve and what the open questions are (see below) and what thinking exercises would be good for Wednesday.
• Monday evening publish the exercises on the Wiki.

For the rest of us:

• Before the Monday lecture (Friday, Saturday, Sunday) check out the lecture script. Work through it and note down mistakes, questions, insights. While doing that think about the following:
  • Is the phrasing correct (read each sentence carefully). Does the sentence mean what is (probably) intended?
  • Think through the steps. How would you solve them algorithmically (e.g. in segment match refinement you might find a statement "for each match in which position x is contained". Such a statement should trigger immediately "How do I find those matches?" Note down solutions or questions.
• On Monday contribute actively. What is not yet clear? What would you like to discuss/do on Friday.
• Before Friday. Think about all the points posted on the Wiki. Be prepared.

Projects

Algorithmic problems in RNA-Seq (1)

(Instructor team: Reinert, Weese, Andreotti, Holtgrewe, Kehr)

In this project you are supposed to work out the idea, applications, algorithms and statistical problems involved in the RNA-Seq method for quantitative transcriptomics. This involves, among others, algorithms and mathematical models for:

• read mapping (suffix arrays and the BW transform)
• repeat resolution
• assignment of expression to splice variants
• …

The core lecture here will be about the general concepts of modern read mappers (filtering, verification, BWT idea)

Algorithmic problems multiple genome comparison (2)

(Instructor team: Reinert, Andreotti, Holtgrewe, Kehr)

In this project you are supposed to work out the idea, applications, algorithms and statistical problems involved in the comparison of different genomes or assemblies. This involves, among others, algorithms and mathematical models for:

• layout of assemblies
• representation of large alignments (a-Bruijn graph, segment refinement and alignment graph).
• computation of large collinear alignments
• computation of non-collinear alignments
• …

The core lecture here will be about the representation of collinear and and non-collinear alignments, segment refinement and the trace heuristics.

Algorithmic problems in HPLC/MS based proteomics (3)

(Instructor team: Reinert, Andreotti, Bielow, Aiche)

In this project you are supposed to work out the idea, applications, algorithms and statistical problems involved in the differential analysis for quantitative proteomics. This involves, among others, algorithms and mathematical models for:

• protein ID
• raw data processing (peak picking, baseline removal, smoothing)
• experimental design of proteomics experiments
• …

The core lecture here will be about peptide and protein ID.

Exam

There will be a usual exam covering the material discussed in the three projects.

date: 23/07/2010 11:00-13:00 T9 SR005

Aktive Teilnahme

I will count the participation as sufficient if the individual software project is functional and the code can be explained.

• Proceedings_of_the_fifth_annual_international_conference_on_Computational_biology_2001_KececiogluSeparating_repeats_in_DNA_sequence.pdf: Kececioglu repeat separation

• Bioinformatics_2002_TammiSeparation_of_nearly_identical_repeats.pdf: Tammi repeat resolution