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1DLoadBalancingConceptualDraft
Parallelism In The SeqAn Library: 1D Load Balancing: Conceptual Draft Open issues * Providing N algorithm states to the forall method instead of just one intr...
r9 - 16 Sep 2010 - 19:15 by KonradRudolph
AdvancedAlgorithms
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 ...
r65 - 23 Mar 2011 - 09:25 by DavidWeese
AdvancedAlgorithms11
Page AdvancedAlgorithms11 Welcome to the Wiki of the Lecture Advanced Algorithms in Bioinformatics (P4). News * 28.09. (Weese): The second examination (Nachkl...
r23 - 01 May 2013 - 18:11 by weese
AdvancedAlgorithms11_Indices
Index Data Structures Lectures Date Lecture* *Materials (Enhanced) Suffix Array 09.05.2011 Suffix Array Construction and Searching script 07...
r21 - 11 Jul 2011 - 15:23 by DavidWeese
AlgLecture10Materials
Here is all the material for the lecture unit 3, lecture 6/6 * Download the script
NEW - 13 Nov 2012 - 12:06 by KnutReinert
AlgLecture10MaterialsWS13
Here is all the material for the lecture unit 3, lecture 5 * Download the lecture notes
r2 - 18 Nov 2013 - 11:40 by AndreottUserTopic
AlgLecture10MaterialsWS14
Here is all the material for the third block (lectures 10 and 11). * Download the lecture notes
NEW - 12 Nov 2014 - 21:29 by RmaerkerUserTopic
AlgLecture11Materials
Here is all the material for the lecture 12 * Download the slides
r3 - 22 Nov 2012 - 08:45 by AlexanderBockmayr
AlgLecture12Materials
Here is all the material for the lecture 12 * Download the slides * Video on Alan Turing at Youtube * Additional material: Characterizing r.e. sets by ge...
r3 - 29 Nov 2012 - 18:26 by AlexanderBockmayr
AlgLecture12MaterialsWS14
Here is all the material for the lecture 12 * Download the slides * Video on Alan Turing
r2 - 20 Nov 2014 - 12:07 by BockmayrUserTopic
AlgLecture13Materials
Here is all the material for the lecture 13 * Download the slides * Additional material: Turing machine codes and a non r.e. language
r3 - 29 Nov 2012 - 18:27 by AlexanderBockmayr
AlgLecture13MaterialsWS13
Here is all the material for turing machines pt. 1. * Download the lecture notes
NEW - 25 Nov 2013 - 11:41 by anduryl
AlgLecture13MaterialsWS14
Here is all the material for the lecture 13 * Download the slides * Additional material 1 : Turing machines as enumerators * Additional material 2 : Unde...
r3 - 26 Nov 2014 - 16:33 by BockmayrUserTopic
AlgLecture14Materials
Here is all the material for the lecture 14 * Download the slides
r2 - 03 Dec 2012 - 17:32 by AlexanderBockmayr
AlgLecture14MaterialsWS13
Here are the materials for turing machines pt. 2 definition of run time analysis. * Download the lecture notes
NEW - 03 Dec 2013 - 16:36 by anduryl
AlgLecture14MaterialsWS14
Here is all the material for the lecture 14 * Download the slides
r2 - 01 Dec 2014 - 16:37 by BockmayrUserTopic
AlgLecture15Materials
Here is all the material for the lecture 15 * Download the slides
r2 - 06 Dec 2012 - 12:48 by AlexanderBockmayr
AlgLecture15MaterialsWS13
Here are the notes about polynomial reductions, NP, NP completeness and some examples. * Download the lecture notes
NEW - 03 Dec 2013 - 16:37 by anduryl
AlgLecture15MaterialsWS14
Here is all the material for the lecture 15 * Download the slides
NEW - 01 Dec 2014 - 16:40 by BockmayrUserTopic
AlgLecture16Materials
Here is all the material for the lecture 16 * Download the slides
NEW - 06 Dec 2012 - 12:47 by AlexanderBockmayr
AlgLecture1Materials
Here is all the material for the lecture unit 1, lecture 1 * Download the script
r3 - 30 Oct 2012 - 15:57 by KnutReinert
AlgLecture1MaterialsWS13
Here is all the material for the lecture unit 1, lecture 1 * Download the script
r4 - 11 Oct 2013 - 16:52 by anduryl
AlgLecture1MaterialsWS14
Here is all the material for the first block (lectures 1 and 2). * Download the lecture notes * Chapter of Motwani book * Review paper by Karp: Randomize...
r3 - 14 Oct 2014 - 08:51 by ReinertUserTopic
AlgLecture2Materials
Here is all the material for the lecture unit 1, lecture 2 * Download the script
r2 - 04 Oct 2013 - 11:51 by ReinertUserTopic
AlgLecture2MaterialsWS13
Here is all the material for the lecture unit 1, lecture 2 * Download the lecture notes
NEW - 17 Oct 2013 - 08:08 by anduryl
AlgLecture3Materials
Here is all the material for Lecture 3 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.1.1 1.3)
NEW - 27 Dec 2012 - 12:22 by AlexanderBockmayr
AlgLecture3MaterialsWS13
Here is all the material for the lecture unit 1, lecture 3 * Download the lecture notes
NEW - 21 Oct 2013 - 16:20 by anduryl
AlgLecture3MaterialsWS14
Here is all the material for Lecture 3 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.1.1 1.3)
NEW - 20 Oct 2014 - 11:07 by BockmayrUserTopic
AlgLecture4Materials
Here is all the material for Lecture 4 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.4.2 4.4)
NEW - 27 Dec 2012 - 12:23 by AlexanderBockmayr
AlgLecture4MaterialsWS13
Here is all the material for the lecture unit 2, lecture 1 * Download the lecture notes
NEW - 24 Oct 2013 - 09:18 by ReinertUserTopic
AlgLecture4MaterialsWS14
Here is all the material for Lecture 4 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.4.2 4.4) * Some history
r2 - 28 Oct 2014 - 09:59 by BockmayrUserTopic
AlgLecture5Materials
Here is all the material for Lecture 5 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.3.1,3.2,3.4)
NEW - 27 Dec 2012 - 12:24 by AlexanderBockmayr
AlgLecture5MaterialsWS13
Here is all the material for the lecture unit 2, lecture 2\ For script see previous lecture.
r2 - 30 Oct 2013 - 19:26 by ReinertUserTopic
AlgLecture5MaterialsWS14
Here is all the material for Lecture 5 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.3.1,3.2,3.4)
NEW - 27 Oct 2014 - 14:32 by BockmayrUserTopic
AlgLecture6Materials
Here is all the material for the lecture unit 2, lecture 4/5 * Download the script
r3 - 05 Nov 2012 - 13:18 by KnutReinert
AlgLecture6MaterialsWS13
Here is all the material for the lecture unit 3, lecture 1 * Download the lecture notes
r3 - 18 Nov 2013 - 13:11 by AndreottUserTopic
AlgLecture6MaterialsWS14
Here is all the material for the third block (lectures 6 and 7). * Download the lecture notes
NEW - 29 Oct 2014 - 13:19 by ReinertUserTopic
AlgLecture7Materials
Here is all the material for the lecture unit 2, lecture 4/5 * Download the script
NEW - 05 Nov 2012 - 13:17 by KnutReinert
AlgLecture8Materials
Here is all the material for the lecture unit 3, lecture 3/4 * Download the script
r2 - 12 Nov 2012 - 09:19 by KnutReinert
AlgLecture8MaterialsWS13
Here is all the material for the lecture unit 3, lecture 3 * Download the lecture notes
NEW - 05 Nov 2013 - 14:31 by AndreottUserTopic
AlgLecture8MaterialsWS14
Here is all the material for the third block (lectures 8 and 9). * Download the lecture notes
NEW - 05 Nov 2014 - 15:48 by ReinertUserTopic
AlgLecture9Materials
Here is all the material for the lecture unit 3, lecture 3/4 * Download the script
r2 - 13 Nov 2012 - 12:05 by KnutReinert
AsperaDownloads
AsperaDownloads Aspera is a company that provides the fasp protocol which uses UDP for file transfer and is much faster than FTP over TCP. The protocol is proprie...
NEW - 25 Jun 2013 - 12:56 by HoltgrewUserTopic
AssemblyComparison
Original goal: 1. Download the reads from a fairly well finished genome Human chr.21 2. and assemble it using two or more standard assemblers e.g. Cel...
r4 - 20 Jul 2010 - 01:28 by sabrina7
AssignmentWeek1
General information for programming exercises * Each group gets access to a svn directory at https://svn.mi.fu berlin.de/agbio/advancedAlgo/SS12/GroupX (Groups...
r8 - 30 Apr 2012 - 12:57 by SandroAndreotti
AssignmentWeek2
Sign up at ProgrammingGroupList for one of the exercises on Tuesday 15th and Wednesday 16th Exercise 2 Read mapping with QUASAR Deadline: 23.05.2012 9:00 a.m. Im...
r5 - 20 May 2012 - 16:21 by SandroAndreotti
AssignmentWeek3
Sign up at ProgrammingGroupList for one of the exercises on Tuesday 12th and Wednesday 14th Exercise 3 Compression with BWT Deadline: 24.06.2012 6:00 p.m. Implem...
r5 - 12 Jun 2012 - 12:13 by SandroAndreotti
BScBlastInSeqAnProject
Eine vergleichende Studie von BLAST Algorithmen Aufgabenstellung BLAST (Basic Local Alignment Tool) ist das bekannteste Programm zur Identifizierung von lokalen ...
r3 - 14 Jul 2013 - 23:16 by annkatrin
BScEfficientExactMotifDiscovery
BScEfficientExactMotifDiscovery Implementation of an existing motif discovery algorithm in SeqAn. Background The goal of motif finding is the detection of novel...
NEW - 06 Jun 2013 - 14:02 by HoltgrewUserTopic
BScGenAlignGraphs
BScGenAlignGraphs Comparing graphs for genome alignment of multiple sequences under the presence of large structural events. Schedule Moritz Finishing Date ...
r9 - 19 Sep 2013 - 15:22 by kiekemo
BScParallelBamIO
BScParallelBamIO Implementation of parallel de /compression of BAM files. * Parallel Bam I/O Schedule/Report Background BAM 1 files are used for storing ali...
r5 - 21 Oct 2013 - 11:08 by HoltgrewUserTopic
BeverageOrder
OUTDATED! Do not use. Page BeverageOrder We plan to regularly order beverages and others from https://www.durstexpress.de Please fill in your orders and give t...
r435 - 01 Oct 2019 - 17:35 by KasseckeUserTopic
BoSSADraft
Page BoSSADraft This page describes the current draft of a Benchmark of Seeds for Sequence Analysis. Sources of inspiration are Rabema, PAPI and Pizza Chili Corpu...
r13 - 22 Jun 2011 - 15:30 by EnricoSiragusa
BscImprovementsOfGraphBasedRealignment
BscImprovementsOfGraphBasedRealignment Improving the Graph Based Realignment in SeqAn. Background The SeqAn library contains a powerful method for realignment an...
r3 - 20 Jun 2013 - 10:19 by HoltgrewUserTopic
BscSeqAn010Seeds
Implementing 01*0 seed search strategy using the bidirectional FM index in SeqAn Background Approximate string matching is an important subtask in many bioinform...
r3 - 25 Nov 2016 - 15:08 by cpockrandt
BscSeqAnAppInBrowser
BscSeqAnAppInBrowser Possible Project for a BSc Thesis in Bioinformatics or Computer Science Introduction Since modern web browsers are used for all kinds of tas...
NEW - 06 Oct 2015 - 18:53 by h4nn3s
BscTreeBasedMapAlignment
BscTreeBasedMapAlignment B.Sc. topic proposal in high throughput proteomics Focus * Programming: ** * Math: ** * Biology: * Introduction LC MS data i...
NEW - 25 Apr 2017 - 17:09 by BielowUserTopic
Carsonella_reanotation
Page Reanotation of the genome of Carsonella Ruddii using non collinear methods Description will follow shortly Layout of project * Identification of a set of...
r13 - 09 Jul 2010 - 00:35 by ivankel
ChipSeqAnalysis
MSc Thesis #8211; Analysis of protein DNA interactions from ChIP seq data Remark This thesis will be a joint project of the Algorithmische Bioinformatik group a...
NEW - 06 Nov 2012 - 22:15 by SandroAndreotti
CompMethodsWS11
Page CompMethodsWS11 In this seminar, we will focus on two different kinds of high throughput technologies: * second generation DNA sequencing * liquid chr...
r17 - 24 Feb 2012 - 09:22 by ChrisBielow
DfgWorkPackages
Page DfgWorkPackages This is the list of work packages from the DFG project. Design and verification of a suitable model for cross species genome compari son (...
NEW - 07 Jan 2010 - 09:03 by KnutReinert
DiscretMathWS10
Page DiscretMathWS10 Welcome to the Wiki of the Lecture Discrete Mathematics News 23.3.2011 (Andreotti): Termin Nachklausur 15.4.2011, 12 14, SR006 Takustr. 9 ...
r26 - 04 Aug 2011 - 09:52 by SandroAndreotti
DiscretMathWS11
Page DiscretMathWS11 Welcome to the Wiki of the Lecture Discrete Mathematics News 6.7.2012 (Reinert): The results of the second exam are online. 29.3.2012 (...
r20 - 16 Jul 2012 - 11:09 by KnutReinert
EclipsePluging
BSc Thesis: Developing an Eclipse plugin for SeqAn Motivation SeqAn is an open source C library of efficient algorithms and data structures for the analysis of ...
r2 - 25 Oct 2011 - 21:00 by BjoernKahlert
ExamPreparation
Page ExamPreparation Rooms: 14:00 16:00 Arnimallee 6 SR 031 16:00 18:00 Takustr. 9 R 006 Questions and topics Please put your questions or things you want t...
r6 - 09 Feb 2012 - 20:12 by elamrani
Expose
Page Expose An expose for the Master's Thesis: "Journal Set: A container for utilizing Incremental Index Structures". Abstract In this Master's Thesis the concep...
r7 - 27 May 2010 - 17:37 by RmaerkerUserTopic
FMIndex
Page FMIndex TITLE TITLE Student Jochen Singer Academic Advisor Prof. Dr. Knut Reinert, David Weese Expose Recent developments in the field of DN...
r11 - 27 Jun 2011 - 13:46 by JochenSinger
ForumSpace
Page ForumSpace Thsi page will be the discussion forum. Lecture 1 REINERT (30.4): Hier könnte eine ausgearbeitetere Version der Vorlesungsabfolge stehen. Oder ...
r34 - 02 Jun 2010 - 17:45 by DavidWeese
ForumSpaceP2
Page ForumSpaceP2 This page will be the discussion forum. Comments to the proposal talk on April 21 Here are some additional comments that haven't been made in t...
r5 - 07 May 2010 - 09:40 by heeger
GenomeComparisonP4
Page GenomeComparisonP4 This is the project page of the Genome Comparison group. Students Mail an alle Gruppenmitglieder: AA2010SS GenComp bei lists.spline.de ...
r39 - 19 Jul 2010 - 18:50 by homilius
GenomeEvolutionSimulator
MSc Thesis: Simulation of Genomes and Genome Evolution Also see the attached PDF file with figures. Motivation The explosion of the availability of genomic data ...
r2 - 29 Jun 2011 - 15:44 by ManuelHoltgrewe
Genomics12
Page Genomics12 Welcome to the Wiki of the MSc lecture Genomics. News The 2nd exam will be on May 13th (Monday), 10 12h, room 049 / Takustr. 9 Bonus Review: Ther...
r37 - 17 Apr 2013 - 12:40 by KasseckeUserTopic
GenomicsLecture1Materials
Here is all the material for the lecture unit 1, lecture 1 The lecture introduces you to the basic sequencing techniques used in genomics analysis. * Download ...
r3 - 21 Oct 2012 - 19:14 by dim
GenomicsLecture2Materials
Here is all the material for the lecture unit 1, lecture 2 * Download the script
r4 - 21 Oct 2013 - 21:16 by ReinertUserTopic
GenomicsLecture2MaterialsWS13
Here is all the material for the lecture unit 1, lecture 2 * Download the script
r2 - 22 Oct 2013 - 13:10 by ReinertUserTopic
GenomicsLecture3Materials
Here is all the material for the lecture unit 1, lecture 3 * Watch a previous lecture as a video: HD (about 0.5 GB or in lower res. * Download the script ...
r3 - 29 Oct 2012 - 17:52 by KnutReinert
GenomicsLecture3MaterialsWS13
Here is all the material for the lecture unit 1, lecture 3 * Watch a previous lecture as a video: HD (about 0.5 GB or in lower res. * Download the script
NEW - 28 Oct 2013 - 16:24 by weese
GenomicsLecture4Materials
Here is all the material for the lecture unit 1, lecture 4 * Watch a previous lecture as a video: HD or in lower res * Download the script * Download the E...
r4 - 12 Nov 2012 - 09:29 by KnutReinert
GenomicsLecture4MaterialsWS13
Here is all the material for the lecture unit 1, lecture 4 * Watch a previous lecture as a video: HD or in lower res * Download the script
NEW - 28 Oct 2013 - 16:38 by weese
GenomicsLecture5Materials
Here is all the material for the lecture unit 1, lecture 5 * Watch a previous lecture as a video: HD or in lower res * Download the script * Download the ...
r4 - 19 Nov 2013 - 09:55 by ReinertUserTopic
GenomicsLecture5MaterialsWS13
Here is all the material for the lecture unit 1, lecture 5 * Watch a previous lecture as a video: HD or in lower res * Download the script
NEW - 19 Nov 2013 - 09:56 by ReinertUserTopic
GenomicsLecture6Materials
Here is all the material for the lecture unit 2, lecture 1 * Download the script * Exercises are in the lecture unit 2, lecture 2
r2 - 30 Nov 2012 - 20:14 by dim
GenomicsLecture6MaterialsWS13
Here is all the material for the lecture * Download the script
NEW - 02 Dec 2013 - 09:30 by jsinger
GenomicsLecture7Materials
Here is all the material for the lecture unit 2, lecture 2 * Download the script * Genomics Exercise 6.pdf: 6th Exercise sheet
r2 - 30 Nov 2012 - 20:15 by dim
GenomicsLecture8Materials
Page GenomicsLecture8Materials Here is all the material for lecture 8, variant calling * Download the script * Download the Exercises ((short description wh...
r2 - 14 Dec 2012 - 12:17 by probins
HowToImproveYourWriting
How To Improve Your Slides, Articles etc. This document aims to help to circumvent some pitfalls in data presentation and creating scientific articles and slides....
r5 - 23 Sep 2019 - 15:30 by KasseckeUserTopic
InitialSetup
Content according to Studienordnung Es werden vertieft Themen aus folgenden Gebieten behandelt: * Verfahren für exaktes und approximatives Suchen in Strings, F...
NEW - 11 May 2010 - 21:29 by KnutReinert
JournalClubS16
Journal Club, SoSe 2016 (19402911, vormals 19401311) Welcome to the Wiki of the Journal Club In this seminar we will present original work in Computational biolog...
r6 - 04 Apr 2016 - 09:13 by ReinertUserTopic
KnimeSec
General info n this part of the Practical course sequence analysis you will be confronted with the situation of integrating several NGS analysis programs (which ...
r18 - 03 Jul 2013 - 09:54 by aiche
Lecture10Materials
Here is all the material for the lecture unit 3, lecture 4 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see pre...
NEW - 01 Jun 2012 - 16:29 by KnutReinert
Lecture11Materials
Here is all the material for the lecture unit 3, lecture 5 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see her...
NEW - 13 Jun 2012 - 10:13 by KnutReinert
Lecture11MaterialsOptWS12
Here is all the material for the lecture 11 * Download the slides * Recommended reading: article by Lustig/Puget (2001)
r2 - 29 Jan 2013 - 09:39 by AlexanderBockmayr
Lecture11MaterialsOptWS14
Here is all the material for the lecture 11 * Download the slides * Recommended reading: article by Lustig/Puget (2001)
r2 - 25 Jan 2016 - 11:58 by BockmayrUserTopic
Lecture12Materials
Here is all the material for the lecture unit 4, lecture 1 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see her...
NEW - 13 Jun 2012 - 10:14 by KnutReinert
Lecture12MaterialsOptWS12
Here is all the material for the lecture 12 * Download the slides * Recommended survey article: Sect.2.4 2.5, Sect.3
r2 - 06 Feb 2013 - 15:45 by AlexanderBockmayr
Lecture12MaterialsOptWS14
Here is all the material for the lecture 12 * Download the slides
NEW - 28 Jan 2015 - 16:18 by BockmayrUserTopic
Lecture13Materials
Here is all the material for the lecture unit 5, lecture 2 * Watch lecture as a video: Watch lecture as a video: here * For the script see here
r3 - 04 Jul 2012 - 10:55 by BirteKehr
Lecture13MaterialsOptWS12
Here is all the material for the lecture 13 * Download the slides * Recommended survey article: Sect.2
r2 - 06 Feb 2013 - 15:44 by AlexanderBockmayr
Lecture13MaterialsOptWS14
Here is all the material for the lecture 13 * Download the slides * Recommended survey article
NEW - 02 Feb 2015 - 10:53 by BockmayrUserTopic
Lecture14Materials
Here is all the material for the lecture unit 5, lecture 3 * For the script see here
NEW - 04 Jul 2012 - 10:58 by BirteKehr
Lecture14MaterialsOptWS12
Here is all the material for the lecture 14 * Download the slides * Recommended survey article
r2 - 07 Feb 2013 - 12:07 by AlexanderBockmayr
Lecture14MaterialsOptWS14
Here is all the material for the lecture 14 * Download the slides * Recommended survey article
NEW - 04 Feb 2015 - 12:36 by BockmayrUserTopic
Lecture15Materials
Here is all the material for the lecture unit 5, lecture 4 * For the script see here
NEW - 04 Jul 2012 - 12:50 by BirteKehr
Lecture15MaterialsOptWS12
Here is all the material for the lecture 15 * Download the slides * Additional material: Article Data
r3 - 09 Feb 2015 - 13:58 by BockmayrUserTopic
Lecture15MaterialsOptWS14
Here is all the material for the lecture 15 * Download the slides * Additional material: Article Data
NEW - 09 Feb 2015 - 14:10 by BockmayrUserTopic
Lecture16Materials
Here is all the material for the lecture unit 4, lecture 2 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * For the script see her...
NEW - 25 Jun 2012 - 19:05 by KnutReinert
Lecture17Materials
Here is all the material for the lecture unit 5, lecture 1 * Watch lecture as a video: The video file was unfortunately corrupted. * For the script see here...
r2 - 29 Jun 2012 - 09:55 by KnutReinert
Lecture1Materials
Here is all the material for the lecture 1 * Download the slides
r13 - 12 Dec 2012 - 18:31 by SandroAndreotti
Lecture1MaterialsOptWS12
Here is all the material for the lecture 1 * Download the slides * Additional material: Kolman/Beck, Linear programming, Chap.1.3 1.4 (click on pdf)
r2 - 18 Dec 2012 - 09:34 by AlexanderBockmayr
Lecture1MaterialsOptWS13
Here is all the material for the lecture unit 1, lecture 1 * Download the script
NEW - 09 Dec 2013 - 16:48 by anduryl
Lecture1MaterialsOptWS14
Here is all the material for the lecture 1 * Download the slides * Additional material: Kolman/Beck, Linear programming, Chap.1.3 1.4 (click on pdf)
NEW - 08 Dec 2014 - 12:48 by BockmayrUserTopic
Lecture2Materials
Here is all the material for the lecture unit 1, lecture 2 * Watch lecture as a video: HD (about 0.5 GB or in lower res. * Download the script * Downloa...
r6 - 29 May 2012 - 15:40 by SandroAndreotti
Lecture2MaterialsOptWS12
Here is all the material for the lecture 2 * Download the slides
r3 - 17 Dec 2012 - 17:25 by AlexanderBockmayr
Lecture2MaterialsOptWS14
Here is all the material for the lecture 2 * Download the slides
r2 - 15 Dec 2014 - 15:24 by BockmayrUserTopic
Lecture3Materials
Here is all the material for Lecture 3 * Download script (see Lecture 2). * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.1.1 1.3)
r7 - 05 Jan 2013 - 11:13 by KnutReinert
Lecture3MaterialsOptWS12
Here is all the material for the lecture 3 * Download the slides
r2 - 17 Dec 2012 - 17:28 by AlexanderBockmayr
Lecture3MaterialsOptWS14
Here is all the material for the lecture 3 * Download the slides
NEW - 15 Dec 2014 - 15:25 by BockmayrUserTopic
Lecture4Materials
Here is all the material for Lecture 4 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.4.2 4.4)
r5 - 05 Jan 2013 - 11:13 by KnutReinert
Lecture4MaterialsOptWS12
Here is all the material for the lecture 4 * Download the slides
r3 - 20 Dec 2012 - 14:08 by AlexanderBockmayr
Lecture4MaterialsOptWS14
Here is all the material for the lecture 4 * Download the slides
NEW - 17 Dec 2014 - 17:18 by BockmayrUserTopic
Lecture5Materials
Here is all the material for Lecture 5 * Download slides * Download lecture notes by A. Schrijver, CWI Amsterdam (Chap.3.1,3.2,3.4)
r6 - 05 Jan 2013 - 11:22 by KnutReinert
Lecture6Materials
Here is all the material for the lecture unit 2, lecture 3 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script ...
r3 - 05 Nov 2012 - 13:16 by KnutReinert
Lecture7Materials
Here is all the material for the lecture unit 3, lecture 1 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script
NEW - 22 May 2012 - 08:32 by KnutReinert
Lecture8Materials
Here is all the material for the lecture unit 3, lecture 2 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script
r2 - 22 Apr 2013 - 21:15 by ReinertUserTopic
Lecture9Materials
Here is all the material for the lecture unit 3, lecture 3 * Watch lecture as a video: Watch lecture as a video: HD or in lower res * Download the script
r2 - 30 May 2012 - 17:34 by KnutReinert
MultiSplitMappingNGS
Multi Split Mapping of NGS reads for variant detection Student Kathrin Trappe Academic Advisor Prof. Dr. Knut Reinert, Anne Katrin Emde Expose The goal ...
r14 - 02 May 2013 - 12:21 by KtrappeUserTopic
OldContent
Online String Searching and Filtering 11.04. 06.05. Index Data Structures 09.05. 30.05. Review 1 11.05. Genome Comparison and RNA Analysis 03.0...
NEW - 19 Mar 2012 - 09:31 by KnutReinert
PMSB_OpenMS_2011
Projektmanagement im Softwarebereich OpenMS 2011 Wiki Seite zum Praktikum Projektmanagement im Softwarebereich http://www.openms.de/ OpenMS 2011. Zeitplan...
r13 - 19 May 2011 - 15:04 by ChrisBielow
PSMB_Seqan_2015_p4
PSMB_Seqan_2015_p4 Introduction Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. It cleaves peptide ...
r3 - 01 Apr 2015 - 14:48 by esiragusa
PSMB_Seqan_2015_p5
PSMB_Seqan_2015_p5 Introduction The q gram(k mer) Index in seqan allows looking up k mers over the index in constant time. However it has two limitations. The fi...
r12 - 26 Mar 2015 - 19:34 by CxpanUserTopic
PSMB_Seqan_2016_p1
PSMB_Seqan_2016_p1 PMSB Project with possible Bachelor Project. Some experience with Javascript is required, some experience with C or C is recommended. Introdu...
NEW - 26 Jan 2016 - 16:41 by h4nn3s
PSMB_Seqan_2016_p2
Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Throug...
r3 - 27 Jan 2016 - 19:16 by kjk
PSMB_Seqan_2017_p1
Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Throug...
NEW - 08 Feb 2017 - 11:28 by kjk
PSMB_Seqan_2017_webassembly
PSMB_Seqan_2017_webassembly PMSB Project at the intersection of C , High performance computing and modern web technologies. Has the possibility to be continued as...
NEW - 01 Feb 2018 - 14:32 by h4nn3s
PSMB_Seqan_fft
Detection of homologous regions with FFT Given a set of sequences your task is to compute homologous segments for all pairs of the input set. The detection of hom...
r2 - 13 Feb 2018 - 16:00 by troja
ProgrammingExerciseOptiWS12
General information for programming exercises * We will continue working in the repository from the Algorithms lecture. To discriminate the exercise files we a...
r12 - 10 Dec 2013 - 14:35 by annikaroehl
ProgrammingExerciseOptiWS13
Short Overview The practical exercises for the lecture Optimization won't be programming exercises. Mostly you have to get familiar with an LP Solver, try to solv...
r11 - 17 Dec 2015 - 11:47 by annikaroehl
ProgrammingExercises
General information for programming exercises * Each group gets access to a svn directory at https://svn.imp.fu berlin.de/agbio/AlgorithmsWS12/GroupX (Enter yo...
r39 - 06 Dec 2012 - 14:27 by SandroAndreotti
ProgrammingExercisesWS13
General information for programming exercises * Each group gets access to a svn directory at https://svn.imp.fu berlin.de/agbio/AlgorithmsWS13/GroupX * The...
r9 - 17 Nov 2013 - 16:31 by AndreottUserTopic
ProgrammingExercisesWS14
General information for programming exercises * Please note, that there will be an optional C crash course on Friday during the exercises. * Please, fill...
r9 - 17 Dec 2015 - 18:08 by annikaroehl
ProgressReportEmde-04-2010
Page ProgressReportEmde 04 2010 Progress report Accomplishments in the last six months: General: * Read many papers on variant detection, notes taken here. ...
r2 - 15 Apr 2010 - 13:30 by KnutReinert
ProgressReportEmde-10-2010
Page ProgressReportEmde 10 2010 Progress Report Accomplishments in the last six months: Split read mapping: * Finished implementation of splitRazers, poster...
r6 - 18 May 2011 - 12:01 by AnneKatrinEmde
ProgressReportSiragusaFall2010
Page ProgressReportSiragusaFall2010 This is the progress report of Enrico Siragusa for the Fall 2010. Accomplishments up to the Fall 2010 * Familiarized with ...
r5 - 07 Dec 2010 - 13:38 by EnricoSiragusa
ProgressReportSiragusaSpring2011
Page ProgressReportSiragusaSpring2011 This is the progress report of Enrico Siragusa for the Spring 2011. Accomplishments up to the Fall 2010 Literature Seeds ...
r6 - 24 May 2011 - 14:10 by EnricoSiragusa
ProtLec0MaterialsWS14
Learning units No learning units for the introductory lecture. Please see the materials for Lecture 1 for the first units. Lectures 00_CPM_WS14_Introduction 00_C...
r7 - 21 Oct 2014 - 15:14 by JpfeufferUserTopic
ProtLec1MaterialsWS14
Learning units Learning unit 1A to Introduction to Proteomics and Metabolomics Learning unit 1B to Overview of separation techniques Learning unit 1C to Introduct...
r9 - 24 Oct 2014 - 15:27 by liangoaix
ProtLec2MaterialsWS14
Learning units Learning unit 2A to Chromatography (updated) Learning unit 2B to Mass spectrometry Lecture slides Lecture slides Exercises Exercises about separ...
r6 - 06 Nov 2014 - 12:40 by JpfeufferUserTopic
ProteomicsVL_WS14
Forschungsmodul: Proteomics VL UE (WiSe 2014) Welcome to the Wiki of the MSc lecture Proteomics (VL: 19400901, UE: 19400902) In this lecture we will cover the ba...
r17 - 03 Feb 2015 - 16:53 by JpfeufferUserTopic
QualityTrim
//
================================================================ // quality_trimmer // ===================================...r2 - 12 Jun 2013 - 09:24 by jsinger
QuantProtP4
Page QuantProtP4 This is the project page of the quantitative proteomics group. Students Mail an alle Gruppenmitglieder: AA2010SS QuantProt bei lists.spline.de ...
r38 - 28 Jul 2010 - 10:32 by ChrisBielow
QuantProtP4_AMS
AMS 3.0 predicting post translational modification sites Material Paper http://www.biomedcentral.com/1471 2105/11/210/abstract OpenMS docu: http://www bs2....
r5 - 22 Jun 2010 - 13:59 by ChrisBielow
QuantProtP4_Elution
Page QuantProtP4_Elution Project Planning for QuantProtP4 Elution Profile comparison Status Stefan * implement a C code (Main.C, see attachment) to det...
r15 - 19 Jul 2010 - 12:05 by StefanMendt
RNA_Bioinformatics
RNA Bioinformatics (S) (19401111), SoSe 2016 Welcome to the Wiki of the seminar RNA Bioinformatics. PLEASE NOTE THAT WE WILL USE THE NEW KVV SYSTEM. CLICK HERE to...
r3 - 04 Mar 2016 - 15:38 by ReinertUserTopic
Razers2Revision
Page Razers2Revision General Points TODO: Wait for evaluation of Hobbes on human, execute class, update tables. Manuel : Section S5 was updated to reflect the u...
r33 - 03 Jul 2012 - 09:26 by KnutReinert
ResearchCooperations
Research Cooperations The Reinert group at FU Berlin maintains research cooperations with German and international research groups. Note that this list here is no...
NEW - 06 May 2011 - 10:31 by ManuelHoltgrewe
ResearchLogReneMaerker
Algorithm Engineering for High Throughput Sequencing Data Summary During the last five years modern sequencing technologies have brought a super exponential grow...
r12 - 19 Aug 2011 - 10:37 by ReneMaerker
ResearchLogTemesgenDadi
Metagenomics. Background Metagenomics is the study of genetic material (metagenome) recovered directly from environmental samples. In these environmental samples...
r3 - 20 Mar 2014 - 09:12 by dadi
RnaSeqP4
Page RnaSeqP4 This is the project page of the RNA Seq group. Students Mail an alle Gruppenmitglieder: AA2010SS RNASeq bei lists.spline.de Name email Cori...
r51 - 22 Jul 2010 - 16:30 by cblasse
SIMDDpAlgo
SIMDDpAlgo SIMD extension of the standard DP algorithms in SeqAn Introduction Newer processors are shipped with 16 registers having an extended width of 128 bit ...
r2 - 12 Mar 2015 - 23:08 by RmaerkerUserTopic
SS13Lecture10Materials
Here is all the material for the lecture 10 * Download the script
r3 - 07 Jul 2014 - 23:19 by weese
SS13Lecture11Materials
Here is all the material for the lecture 11 * Download the script
NEW - 11 Jul 2013 - 23:38 by AndreottUserTopic
SS13Lecture12Materials
The lecture on Thursday 4.7.2013 will start 10:30 Here is all the material for the lecture 9 * Download the script
r3 - 11 Jul 2013 - 23:38 by AndreottUserTopic
SS13Lecture13Materials
Here is all the material for the lecture 11 * Download the script
NEW - 03 Jul 2013 - 11:23 by ReinertUserTopic
SS13Lecture1Materials
Here is all the material for the lecture 1 * Download the script.pdf
r3 - 04 Apr 2015 - 12:53 by ReinertUserTopic
SS13Lecture2Materials
Here is all the material for the lecture 1 * See lecture 1
NEW - 05 Apr 2013 - 12:45 by ReinertUserTopic
SS13Lecture3Materials
Here is all the material for the lecture 3 * Download the script.pdf * Watch a previous lecture as a video lower res or high res
r4 - 27 Apr 2015 - 10:13 by ReinertUserTopic
SS13Lecture4Materials
Here is all the material for the lecture 4 * Download the script * exercise_4.pdf
r3 - 04 Apr 2015 - 13:04 by ReinertUserTopic
SS13Lecture5Materials
Here is all the material for the lecture 5 and 6 * Download the script
r4 - 20 May 2014 - 14:46 by weese
SS13Lecture6Materials
Here is all the material for the lecture 6 * Download the script
r3 - 16 May 2014 - 12:35 by weese
SS13Lecture7Materials
Here is all the material for the lecture 6 * Download the script
r4 - 17 May 2015 - 17:59 by ReinertUserTopic
SS13Lecture8Materials
Here is all the material for the lecture 6 * See last script
r5 - 17 May 2015 - 18:00 by ReinertUserTopic
SS13Lecture9Materials
Here is all the material for the lecture 9 * Download the script
r2 - 10 Jun 2013 - 18:51 by weese
SS14Lecture11Materials
Here is all the material for the lecture 7 and 8 * Download the script:
NEW - 03 Jun 2014 - 09:39 by ReinertUserTopic
SS15Lecture10Materials
Here is all the material for the lecture 12 * Download the script
NEW - 28 May 2015 - 17:14 by ReinertUserTopic
SS15Lecture9Materials
Here is all the material for the lecture 12 * Download the script
r5 - 18 Jun 2015 - 15:27 by ReinertUserTopic
SeedDesign
Page SeedDesign This page contains an essay on the state of the art of seed design. The goal of this essay is to give an unifying view on seed design. Most releva...
r2 - 25 Nov 2010 - 14:49 by EnricoSiragusa
SeqAn
General info n this part of the Practical course sequence analysis you will be confronted with the situation of prototyping NGS analysis programs with an availab...
r8 - 12 Jun 2013 - 12:06 by jsinger
SeqAnRetreat2011
Information about the SeqAn workshop 2011 The SeqAn BioStore website is up. Please find information here.
r8 - 14 Jul 2011 - 22:40 by KnutReinert
SeqAnRetreat2012
Guidelines for the Organization of Meetings Technical Factors * find/reserve a room SeqAn Retreat March 2012 with Illumina: T9/053 * look into technical...
NEW - 29 Feb 2012 - 18:04 by AnjaKasseckert
Sequence_analysis_2015
Sequence Analysis, SoSe 2015 (LV Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of Sequence Analysis. This module consists of 2 hours lectu...
r38 - 07 Jul 2015 - 11:59 by RmaerkerUserTopic
Sequence_analysis_2016
Sequence Analysis, SoSe 2016 *(LV Nr. 19401601 (V), 19401602 (Ü), 19401611 (S)) Welcome to the Wiki of Sequence Analysis. Dear Students. We will use for the lec...
r3 - 04 Mar 2016 - 15:24 by ReinertUserTopic
SlaganSupermap
SLAGAN Input: two genomic dna sequences in FASTA file(s) Generation of local alignments (Svenja) SLAGAN uses the CHAOS aligner for this phase: * finding seeds...
r11 - 12 Jul 2010 - 13:57 by heeger
SnippetsAnneKatrin
Page SnippetsAnneKatrin This is where I write my weekly goals. all time todos: * make splitRazers project page * add link in seqanswers forum srp thread ...
r34 - 07 Dec 2010 - 13:43 by AnneKatrinEmde
SnpStore
Page SnpStore Short overview of SnpStore implementation. General structure Here is a general pseduocode like outline of how SnpStore proceeds. The functionality...
r3 - 25 Sep 2012 - 14:02 by AnneKatrinEmde
SpaceEfficientBWTConstruction
SpaceEfficientBWTConstruction Implementation of a fast and memory efficient BWT construction algorithm. Background The Burrows Wheehler Transform transforms a te...
r7 - 11 Jul 2013 - 16:19 by zer
ThesisApproxHammingMatch
Approximate String Matching (Hamming Distance) This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn...
r4 - 02 Jan 2011 - 22:05 by ManuelHoltgrewe
ThesisGenomesPerMail
Page ThesisGenomesPerMail ((short description what this page is about)) Expose Rene, please write an expose for the thesis here with the following tasks. Task...
r7 - 27 May 2010 - 16:20 by RmaerkerUserTopic
ThesisMCRazer
ThesisMCRazer Check, whether abstract, description, and literature are in CMS Parallelization of RazerS $ Student: Martin Riese $ Academic Advisor: David W...
r4 - 03 Feb 2010 - 09:03 by mriese
ThesisMCRazerSpeedOA
Page ThesisMCRazerSpeedOA what was the used q here? Can you make for a first estimate q =10, q=14, q=22 (f course only in open adressing?) Next question would be,...
r7 - 14 Mar 2010 - 19:18 by mriese
ThesisMeganRazersReports
Page ThesisMeganRazersReports Weekly Reports for the Bachelor Thesis "Comparative Genomics with MEGAN and RazerS" by Hannes Hauswedell Week 1 (2009 07 11..2009 0...
r9 - 29 Sep 2009 - 21:55 by hauswede
ThesisNGSOverlap
Overlap Module for NGS Pipeline Summary The overlap module merges the information retained by read mapping to a genome with annotation information (for example g...
r4 - 16 Aug 2009 - 21:30 by krakau
ThesisNgsCleaning
NGS Data Cleaning TODO: Manuel Note that we can shift the focus of the thesis much stronger towards programming/implementation if you want to program! Next Genera...
r4 - 15 Jun 2012 - 11:00 by KnutReinert
ThesisParallelismInSeqan
Parallelism In The SeqAn Library The purpose of this thesis is to allow "easy parallelism" in the SeqAn library. This will consist of identifying parts of the lib...
r5 - 10 Sep 2010 - 14:50 by ManuelHoltgrewe
ThesisParallelismInSeqanPatterns
Parallelism In The SeqAn Library: Patterns for Parallelization A brief summary of patterns for parallelization, based on Massingill et al. 2000 . Finding Concur...
r12 - 21 Jun 2010 - 15:37 by KonradRudolph
ThesisProposals
Thesis Proposals OUTDATED! Go to: https://kvv.imp.fu berlin.de/x/8RK4cp Here is the section for BSc and MSc students. At the beginning of the thesis the student ...
r3 - 23 Sep 2019 - 11:21 by KasseckeUserTopic
ThesisScalingGenomeAlignment
Scaling genome alignment to hundreds of genomes Topic With the rapid development of next generation sequencing technologies more and more genomes are being seque...
NEW - 19 Mar 2012 - 11:23 by BirteKehr
ThesisScoreMatrix
Substitution Matrix Generation Algorithms This Bachelor thesis gets you in touch with current research for string matching, modern implementation in C /SeqAn, sou...
r2 - 08 Apr 2010 - 14:25 by KnutReinert
VariantDetectionAppliedPapers
Page VariantDetectionAppliedPapers Collection of applied variant detection papers, with comments. Applied Papers Genome wide mapping and assembly of structural ...
NEW - 07 Dec 2010 - 22:35 by AnneKatrinEmde
VariantDetectionPapers
Page VariantDetectionPapers Remarks to papers concerning variant detection in NGS data. Method Papers Simple variation VarScan: variant detection in massively ...
r20 - 18 May 2011 - 13:11 by AnneKatrinEmde
VocabularyAnneKatrin
Page VocabularyAnneKatrin Here I collect pieces of information and "vocabulary" that at some point seemed important. Mixture Models In statistics, a probability ...
NEW - 12 Feb 2010 - 13:30 by AnneKatrinEmde
WebHome
Return to ABI Homepage DEPRECATED! Go to our new wiki https://www.mi.fu berlin.de/en/inf/groups/abi/ Internal infos at https://wikis.fu berlin.de/display/abi/ ...
r114 - 09 Aug 2023 - 16:07 by AdminUser
WholeTranscriptomeAnalysis
MSc Thesis Whole transcriptome and miRNome analysis from next generation sequencing data Remark This thesis will be a joint project of the Algorithmische Bioin...
NEW - 06 Nov 2012 - 22:09 by SandroAndreotti
Worklog_Hauswedell
Page Worklog_Hauswedell Project Work log Hauswedell Friday, 25.06.2010: * second "real" meeting with Thieme to do planning and division of work * got access...
r4 - 06 Jul 2010 - 19:16 by h4nn3s
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