Content: please see the German version.

Studierende der Mathematik (Monobachelor und Lehramt) und Bioinformatik, sowie Numerikinteressierte aus Physik, Informatik und anderen Natur- und Geisteswissenschaften.

Contents:

• models of computation
  • automata
  • formal languates
  • grammars and the Chomsky-hierarchy
  • Turing-machines
  • computabilty
• introduction to the complexity of computational problems

• Uwe Schöning, Theoretische Informatik kurzgefasst, 5. Auflage, Spektrum Akademischer Verlag, 2008
• John E. Hopcroft, Rajeev Motwani, Jeffrey D. Ullman, Einführung in die Automatentheorie, Formale Sprachen und Komplexität, Pearson Studium, 3. Auflage, 2011
• Ingo Wegener: Theoretische Informatik - Eine algorithmenorientierte Einführung, 2. Auflage, Teubner, 1999
• Michael Sipser, Introduction to the Theory of Computation, 2nd ed., Thomson Course Technology, 2006
• Wegener, Kompendium theoretische Informatik - Eine Ideensammlung, Teubner 1996

Content

Database design with ERM/ERDD. Theoretical foundations of relational database systems: relational algebra, functional dependencies, normal forms. Relational database development: SQL data definitions, foreign keys and other integrity constraints, SQL as applicable language: essential language elements, embedding in programming language. Application programming; object-relational mapping. Security and protection concepts. Transaction subject, transactional guaranties, synchronization of multi user operations, fault tolerance features. Application and new developments: data warehousing, data mining, OLAP.

Project: the topics are deepened in an implementation project for student groups.

• Alfons Kemper, Andre Eickler: Datenbanksysteme - Eine Einführung, 5. Auflage, Oldenbourg 2004
• R. Elmasri, S. Navathe: Grundlagen von Datenbanksystemen, Pearson Studium, 2005

Requirements

• ALP 1 - Functional Programming
• ALP 2 - Object-oriented Programming
• ALP 3 - Data structures and data abstractions
• OR Informatik B

Contents

The class focuses on:

• Fundations of programming: imperative and object-oriented programming
• Algorithms and data structures: design and implementation of data structures
• theory of algorithms

We use C++ as an implementation language.

Target Audience

Students with Computer Science as a minor concentration and students of bioinformatics.

• Goodrich, Tamassia: Data Structures and Algorithms in C++
• Stroustrup: Die C++ Programmiersprache
• Cormen, Leiserson, Rivest, Stein: Introduction to Algorithms
• Kleinberg, Tardos: Algorithm Design
• Schöning: Algorithmen - kurz gefasst

Contents:

• number systems: from natural numbers to real numbers, completeness property of the reals
• polynomials: roots of polynomials, polynomial interpolation, rational functions
• special functions:  exponential function, logarithm, trigonometric functions
• complex numbers: exponential function for complex numbers, complex roots
• convergence of sequences and series, convergence of functions, continuous functions
• differential calculus: derivative of a function,  interpretations and applications of the derivative
• intergral calculus: definite and indefinite integrals,  fundamental theorem of calculus, applications
• power series
• Taylor series
• basics of differential calculus for multivariate functions: partial derivative, gradient, Jacobi matrix
• solution of simple  differential equations

• Kurt Meyberg, Peter Vachenauer: Höhere Mathematik 1, Springer-Verlag, 6.Auflage 2001
• Dirk Hachenberger: Mathematik für Informatiker, Pearson 2005
• Gerhard Berendt: Mathematische Grundlagen der Informatik, Band 2, B.I.-Wissenschaftsverlag; 1990
• Thomas Westermann: Mathematik für Ingenieure mit Maple 1, Springer-Verlag, 4.Auflage 2005

Target group:

Students of Bioinformatics (BSc, second semester)

Requirements:

Mathematik für Bioinformatiker I

Content: please see the German version.

Studierende der Mathematik (Monobachelor und Lehramt) und Bioinformatik, sowie Numerikinteressierte aus Physik, Informatik und anderen Natur- und Geisteswissenschaften.

See German text version.

Content

Database design with ERM/ERDD. Theoretical foundations of relational database systems: relational algebra, functional dependencies, normal forms. Relational database development: SQL data definitions, foreign keys and other integrity constraints, SQL as applicable language: essential language elements, embedding in programming language. Application programming; object-relational mapping. Security and protection concepts. Transaction subject, transactional guaranties, synchronization of multi user operations, fault tolerance features. Application and new developments: data warehousing, data mining, OLAP.

Project: the topics are deepened in an implementation project for student groups.

• Alfons Kemper, Andre Eickler: Datenbanksysteme - Eine Einführung, 5. Auflage, Oldenbourg 2004
• R. Elmasri, S. Navathe: Grundlagen von Datenbanksystemen, Pearson Studium, 2005

Requirements

• ALP 1 - Functional Programming
• ALP 2 - Object-oriented Programming
• ALP 3 - Data structures and data abstractions
• OR Informatik B

Contents:

• models of computation
  • automata
  • formal languates
  • grammars and the Chomsky-hierarchy
  • Turing-machines
  • computabilty
• introduction to the complexity of computational problems

• Uwe Schöning, Theoretische Informatik kurzgefasst, 5. Auflage, Spektrum Akademischer Verlag, 2008
• John E. Hopcroft, Rajeev Motwani, Jeffrey D. Ullman, Einführung in die Automatentheorie, Formale Sprachen und Komplexität, Pearson Studium, 3. Auflage, 2011
• Ingo Wegener: Theoretische Informatik - Eine algorithmenorientierte Einführung, 2. Auflage, Teubner, 1999
• Michael Sipser, Introduction to the Theory of Computation, 2nd ed., Thomson Course Technology, 2006
• Wegener, Kompendium theoretische Informatik - Eine Ideensammlung, Teubner 1996

This course covers fundamental concepts of biomedical bioinformatics and genomics, with a particular focus on questions and goals of biomedical data analysis.

Amongst others, the following topics will be treated: genome-wide association studies (GWAS), eQTLs, machine learning and classification of patient data, biomedical ontologies and their application in bioinformatics, hereditary disorders and disease gene prediction, principles of mutation/variant interpretation, principles of computational cancer research.

Further information is available at: http://klinphys.charite.de/bioinfo/

This class is a combination of lectures, student talks and experimental work in the lab.

Topics are:

- basics of biosignal recording, processing, and analyses (e.g. filtering, artifact correction, smoothing, mobile monitoring technologies, validation of new technologies, etc.),
- chronobiology,
- physical activity,
- body composition technologies,
- electrophysiological techniques in epithelial physiology,
- optical methods (microfluorimetric measurements, confocal laser scanning microscopy, super resultion microscopy, freeze fracture electron microscopy),
- homology modelling of protein structure.

Infos zur Veranstaltung: http://klinphys.charite.de/bioinfo/

Infos zur Veranstaltung: http://klinphys.charite.de/bioinfo/

Goals:

The students will gain a deeper unterstanding for basic algorithmic concepts for the analysis of genomic sequencing related to state of the art research in bioinformatics and biotechnology. They will learn various paradigms for the approximate search. They will know which algorithms should be preferred under what circumstances and are able to grasp key concepts of scientific publications related to this field.

Compulsory optional subject in bioinformatics.

Course overview:

This course will take place in the semester break (24.09 - 5.10.2018), 8 days during 2 weeks, daily 10 am - 5 pm

The Structural Bioinformatics Group offers a broad and comprehensive set of lectures in the areas of structural bioinformatics and drug design. The course begins with a general introduction of the drug design pipeline and an introductory course on the structural bioinformatics research field. These lead on to more specialized topics, amongst others in chemo-informatics, molecular docking, homology modeling and more detailed aspects of toxicity prediction models.

Structure of the course:

This course consists of eight lecture series. A detailed lecture for a period of 2 hrs on individual topics is delivered in the morning session. Afternoon session consists of an assignment for each topic. This part of the lecture course is assessed by examination, which will take place at the end of the course. Students are asked to delivered a seminar/presentation for 25 minutes, on the topic assigned to them. The material for the examination will be provided in advance, ensuring that the students have required time for preparation.

Topics for lectures are:

• 1. Introductory session
• 2. Peptide design
• 3. Homology modeling
• 4. 3D Molecular superimposition of small molecules
• 5. In silico screening, molecular fingerprints and chemical similarity
• 6. Molecular docking
• 7. Natural products and fragments based drug discovery
• 8. In silico toxicity prediction

For further information see: http://bioinf-apache.charite.de/main/course_theoretical.php

This course will take place in the semester break.

Block course during the semester break. Suitable dates will be determined by doodle.

For further information: http://klinphys.charite.de/bioinfo/

or mail to Dorothee Günzel

Within this course you will carry out molecular biologic experiments (such as site-directed mutagenesis by using two-step PCR). The construct will be cloned into expression vectors, transformed and amplified in bacteria, extracted, sequenced and overexpressed in cultured cells.

These cells will be analyzed in the confocal laser scanning microscope and by other techniques.

The experimental part will be flanked by seminars introducing the theoretical background and the various techniques.

The exact program of this course depends on the actual research of the institute and is tightly connected to our actual projects.

Goals:

The students are able to use standard programs of sequence analysis independetly. They know various concepts and are able to use and program a chosen system. The students will be able to design new workflows and present the results graphically.

Goals:

The students will be introduced to the basic statistical and algorithmic concepts in the field of Machine Learning, especially in the context of current research in bioinformatics, biology and biotechnology. They will work on several practical problems and implement / use the methods learned during the lectures to extract information from biological datasets in R. In particular, they will learn how to process data, choose the appropriate model to answer specific questions, evaluate and communicate the results. The students will be assigned weekly exercises which they have to complete. Presenting in turns the results from the exercises, in addition to a final oral exam, are prerequisites to pass the course.

Content:

• Pre-processing of biological data and model implementation with R
• Classification metrics and permutation approaches
• Linear Models for Regression and Classification
• Kernel Methods for Regression and Classification - Feature Selection
• Semi-supervised learning / active learning
• Classification trees and Random Forests
• Graphical models

For further information see: http://www.molgen.mpg.de/3434810/Applied-Machine-Learning

Prerequisites:

Attended the Statistics course from the Master in Bioinformatics FU (or equivalent)

Goals:

The students will be introduced to the basic statistical and algorithmic concepts in the field of Machine Learning, especially in the context of current research in bioinformatics, biology and biotechnology. They will work on several practical problems and implement / use the methods learned during the lectures to extract information from biological datasets in R. In particular, they will learn how to process data, choose the appropriate model to answer specific questions, evaluate and communicate the results. The students will be assigned weekly exercises which they have to complete. Presenting in turns the results from the exercises, in addition to a final oral exam, are prerequisites to pass the course.

Content:

• Pre-processing of biological data and model implementation with R
• Classification metrics and permutation approaches
• Linear Models for Regression and Classification
• Kernel Methods for Regression and Classification - Feature Selection
• Semi-supervised learning / active learning
• Classification trees and Random Forests
• Graphical models

For further information see: http://www.molgen.mpg.de/3434810/Applied-Machine-Learning

Prerequisites:

Attended the Statistics course from the Master in Bioinformatics FU (or equivalent)

The goal of the practical course in medical genomics is to learn how to apply state-of-the-art computational and statistical methods for the analysis of high-throughput DNA sequencing data, as it is already done for medical diagnostics. All important steps of the workflow will be covered: the initial quality control, the alignment of sequencing data (reads), and the identification of mutations (variant calling) as well as their annotation and interpretation.

Although the course is aiming at medical applications, the used techniques can be applied also to other fields of research.

Contents:

Reaction diffusion simulations are important tools for the modeling of signal transduction cascades in cellular processes. This seminar consists of lectures for the introduction to reaction-diffusion processes as well as "hands-on" computer exercises in which the particle-based reaction-diffusion simulator ReaDDy (https://readdy.github.io/) will be taught.

For more information see  >>> here

Master students with a background in physics, chemistry, bioinformatics or computer science

Content:

In this seminar we will present original work in Computational biology as well as progress reports from PhD students. Master students will either be assigend a paper, or present their MSc thesis plans and results, or report about their "Fortgeschrittenenpraktikum". Credits are only awarded for the presentation of papers.

Please sign up on the KVV pages (open "Site Browser" and look forJournal Club).

Aktuelle Publikationen aus der Forschung

Open for:

Master and PhD students

In this seminar we will investigate succinct, compact and compressed data structures which have lately become increasingly
more important in Bioinformatics. The best example is the very popular and widely used Compressed Suffix Array (also called FM-index). It uses constant time rank queries on bitvectors, as a replacement for table lookups.

In the seminar we will read original papers and parts of the new book "Compact data structures" by Gonzalo Navarro. The first part of the seminar will consist of chapters of the book reviewing basic techniques. The second part will deal with recent bioinformatics data structures

Gonzalo Navarro: Compact data structures, Cambridge University Press

Comment regarding time conflicts of this module with university exams

Please note that I am happy to excuse your absence in case a University exam is overlapping a morning or afternoon session of this module. In that case, please email me your time conflict(s) as early as possible and provide written evidence for the exam by the registration deadline for this module.

Contents

The last few years have seen an explosion of methods for investigating RNA structures and RNA-RNA interactions. In fact, general methods for examining the RNA structurome and RNA-RNA interactome in vivo were only published in 2016. These methods open exciting possibilities to explore transcriptomes in unprecedented ways.

Many of these methods combine novel experimental pipelines with next-generation sequencing and dedicated computational analysis pipelines in order to make discoveries. Both aspects (experimental and computational) typically require sophisticated protocols that are both key to discovery-making.  The corresponding computational aspects cannot be understood or optimised without considering the experimental side and vice versa.

Topic-wise, our focus will be on:

• algorithms and computational strategies including probabilistic and comparative methods
• transcriptome-wide experimental methods and protocols for investigating RNA structures and RNA-RNA interactions in vitro and in vivo

Target audience

This self-contained module is targeted at both, graduate students in Bioinformatics as well as graduate students in Biochemistry. It thus goes without saying that no participant is expected to know everything. Everyone, however, is expected to learn something outside their "official" area of expertise, as we will cover both computational and experimental methods for investigating RNA structures and RNA-RNA interactions. In-between questions will thus be encouraged throughout.

Format

The module comprises a lecture-part where we will cover the basics you need to know in order to understand the currently existing approaches as well as a seminar-part where you will present and discuss ongoing research in this field as well as a small research proposal of your own. Formally speaking, the module comprises

• lectures
• example classes
• seminar talks

Language

Note that the language for the entire module will be English.

Student participation and important deadlines

The registration deadline for this module is Monday, 19. March 2018. Please note that I am happy to excuse your absence in case a University exam is overlapping a morning or afternoon session of this module. In that case, please email me your time conflict(s) as early as possible and provide written evidence for the exam.

In order to pass the entire module, you need to:

• give one or two presentations (if you wish, you may email me a short list of 4 preferred papers to Irmtraud Meyer by Monday, 19. March, at the very latest; the earlier you send your short-list, the higher your chance of being assigned a paper from your list (i.e. first come, first served); you may work in a team of two and give twice the presentations (as team), in that case both students need to email me to (a) confirm the other team member and (b) the same list of 4 papers; I reserve the right to assign presentations)
• clarify any questions you may have regarding your presentation by Thursday, 5. April, e.g. by emailing the contact person assigned to your paper or by arranging a face-to-face meeting. For this, please contact Stefan or Peter directly (see the list of papers for whom to contact for which paper).
• email your finalized presentation to Irmtraud Meyer by Friday, 6. April, as a single pdf-file
• attend all events (if you miss a class without a formal excuse (e.g. illness, university exam) , you may be asked to write a report)
• participate actively (e.g. by chairing a discussion, asking and/or clarifying questions)
• propose and defend a small potential research project of your own (submit 1-2 pages as pdf-file including references via email to Irmtraud Meyer by Friday, 6. April; this should ideally be done in teams of two)
• come prepared (e.g. read papers ahead of time so you could readily summarize and discuss it)
• provide feedback to fellow students via a small questionnaire to help them improve their presentation skills

For MSc students in Biochemistry: if you want to participate only in the lecture-part of the module, you have to attend all lectures and example classes and actively participate in both to pass it.

What you will learn

• fundamental principles underlying existing computational and experimental methods and their pros and cons
• critically present and discuss research concepts and strategies
• propose and defend a small original research project of your own
• hopefully, think outside the box and learn to address a wider scientific audience
• chair a discussion
• optionally: work in a team of two (presentations, research proposal)

Grading

Grading of the module will be on a pass/fail basis. Note that any teamwork will be judged as a whole.

Dates and location

The entire module will take place on the campus of the Max Delbrueck Centre in Berlin-Buch on workdays (Mo to Fr)

• 9.30 to 16.30 h from 3. April (Tuesday, first day) to 13. April 2018 (Friday, last day).

The research campus offers facilities for lunch and tee/coffee breaks.

• the first week will take place in MDC campus building C81 (FMP) in room 1.14 on the ground floor
• the second week will take place in the library of the MDC campus in building 10 in room 27.1 on the ground floor

see the directions to the MDC campus in Berlin-Buch and a map of the MDC campus.

Contact

In case of general questions including questions regarding the registration for this module, please contact Irmtraud Meyer by email or phone (030-9406-3292). For questions about specific papers, please contact Peter or Stefan directly, see the list of papers.

Background reading

• C.K. Kwok (2016): Dawn of the in vivo RNA structurome and interactome
• J.G. Aw (2016): In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

This seminar will cover central aspects of modern bottom-up proteome analysis by mass spectrometry with a focus on bioinformatic algorithms and data analysis.
    After a brief introduction into the field of mass spectrometry-based proteomics (instrument types, data properties, overview of bioinformatics challenges) we will explore the big cornerstones, including isotope models and averagines, scoring algorithms for the identification of mass spectra, false-discovery-rate estimation using decoy peptides, absolute and relative quantification of proteins and correlation between mRNA and protein expression.

Introductory seminar to computer-aided drug design, including structure- and ligand-based methods. Briefly, computer-aided drug design uses computational chemistry to discover, enhance, or study drugs and related biologically active molecules. In this seminar, the students will independently acquire knowledge about topics in the context of structural bioinformatics. Topics include homology modelling, target assessment, molecular docking, in-silico screening (molecular fingerprints, chemical similarity), ADME and toxicity predictions (QSAR, machine learning), and more.

The students can select a topic from the presented drug development pipeline and (under guidance) will collect material (papers, data and algorithms). At the end of the seminar, they will present the topic as well as an application of such.

It is advisable/helpful (but not mandatory) to attend the practical course ‘Using open source software and libraries for data analysis and computer-aided drug design’ (Volkamer, WiSe 2016/17, block seminar at the end of march) or ‘Current questions of structural bioinformatics’ (Preissner/Banerjee) before.

The set-up of the course will depend on the number of attending students. Preferably, we will have a bi-weekly meeting (half-day) till mid-June, followed by a weekly presentation round (4 dates à 2 hours) till the end of the semester.

More details will be discussed on Thursday, April 26th, 9-11:30 am, Charité, Mitte.

For more information see: AG Volkamer - Teaching

Within this course advance biometrical methods applied within the context of clinical and observational trials are introduced. Issue like complex study designs, sample size (re)calculation and advanced modelling will be addressed among others. Students should have a solid background in statistics and an interest in medical applications of statistics.

Contents:

Reaction diffusion simulations are important tools for the modeling of signal transduction cascades in cellular processes. This seminar consists of lectures for the introduction to reaction-diffusion processes as well as "hands-on" computer exercises in which the particle-based reaction-diffusion simulator ReaDDy (https://readdy.github.io/) will be taught.

For more information see  >>> here

Master students with a background in physics, chemistry, bioinformatics or computer science

Content:

In this seminar we will present original work in Computational biology as well as progress reports from PhD students. Master students will either be assigend a paper, or present their MSc thesis plans and results, or report about their "Fortgeschrittenenpraktikum". Credits are only awarded for the presentation of papers.

Please sign up on the KVV pages (open "Site Browser" and look forJournal Club).

Aktuelle Publikationen aus der Forschung

Open for:

Master and PhD students

In this seminar we will investigate succinct, compact and compressed data structures which have lately become increasingly
more important in Bioinformatics. The best example is the very popular and widely used Compressed Suffix Array (also called FM-index). It uses constant time rank queries on bitvectors, as a replacement for table lookups.

In the seminar we will read original papers and parts of the new book "Compact data structures" by Gonzalo Navarro. The first part of the seminar will consist of chapters of the book reviewing basic techniques. The second part will deal with recent bioinformatics data structures

Gonzalo Navarro: Compact data structures, Cambridge University Press

Comment regarding time conflicts of this module with university exams

Please note that I am happy to excuse your absence in case a University exam is overlapping a morning or afternoon session of this module. In that case, please email me your time conflict(s) as early as possible and provide written evidence for the exam by the registration deadline for this module.

Contents

The last few years have seen an explosion of methods for investigating RNA structures and RNA-RNA interactions. In fact, general methods for examining the RNA structurome and RNA-RNA interactome in vivo were only published in 2016. These methods open exciting possibilities to explore transcriptomes in unprecedented ways.

Many of these methods combine novel experimental pipelines with next-generation sequencing and dedicated computational analysis pipelines in order to make discoveries. Both aspects (experimental and computational) typically require sophisticated protocols that are both key to discovery-making.  The corresponding computational aspects cannot be understood or optimised without considering the experimental side and vice versa.

Topic-wise, our focus will be on:

• algorithms and computational strategies including probabilistic and comparative methods
• transcriptome-wide experimental methods and protocols for investigating RNA structures and RNA-RNA interactions in vitro and in vivo

Target audience

This self-contained module is targeted at both, graduate students in Bioinformatics as well as graduate students in Biochemistry. It thus goes without saying that no participant is expected to know everything. Everyone, however, is expected to learn something outside their "official" area of expertise, as we will cover both computational and experimental methods for investigating RNA structures and RNA-RNA interactions. In-between questions will thus be encouraged throughout.

Format

The module comprises a lecture-part where we will cover the basics you need to know in order to understand the currently existing approaches as well as a seminar-part where you will present and discuss ongoing research in this field as well as a small research proposal of your own. Formally speaking, the module comprises

• lectures
• example classes
• seminar talks

Language

Note that the language for the entire module will be English.

Student participation and important deadlines

The registration deadline for this module is Monday, 19. March 2018. Please note that I am happy to excuse your absence in case a University exam is overlapping a morning or afternoon session of this module. In that case, please email me your time conflict(s) as early as possible and provide written evidence for the exam.

In order to pass the entire module, you need to:

• give one or two presentations (if you wish, you may email me a short list of 4 preferred papers to Irmtraud Meyer by Monday, 19. March, at the very latest; the earlier you send your short-list, the higher your chance of being assigned a paper from your list (i.e. first come, first served); you may work in a team of two and give twice the presentations (as team), in that case both students need to email me to (a) confirm the other team member and (b) the same list of 4 papers; I reserve the right to assign presentations)
• clarify any questions you may have regarding your presentation by Thursday, 5. April, e.g. by emailing the contact person assigned to your paper or by arranging a face-to-face meeting. For this, please contact Stefan or Peter directly (see the list of papers for whom to contact for which paper).
• email your finalized presentation to Irmtraud Meyer by Friday, 6. April, as a single pdf-file
• attend all events (if you miss a class without a formal excuse (e.g. illness, university exam) , you may be asked to write a report)
• participate actively (e.g. by chairing a discussion, asking and/or clarifying questions)
• propose and defend a small potential research project of your own (submit 1-2 pages as pdf-file including references via email to Irmtraud Meyer by Friday, 6. April; this should ideally be done in teams of two)
• come prepared (e.g. read papers ahead of time so you could readily summarize and discuss it)
• provide feedback to fellow students via a small questionnaire to help them improve their presentation skills

For MSc students in Biochemistry: if you want to participate only in the lecture-part of the module, you have to attend all lectures and example classes and actively participate in both to pass it.

What you will learn

• fundamental principles underlying existing computational and experimental methods and their pros and cons
• critically present and discuss research concepts and strategies
• propose and defend a small original research project of your own
• hopefully, think outside the box and learn to address a wider scientific audience
• chair a discussion
• optionally: work in a team of two (presentations, research proposal)

Grading

Grading of the module will be on a pass/fail basis. Note that any teamwork will be judged as a whole.

Dates and location

The entire module will take place on the campus of the Max Delbrueck Centre in Berlin-Buch on workdays (Mo to Fr)

• 9.30 to 16.30 h from 3. April (Tuesday, first day) to 13. April 2018 (Friday, last day).

The research campus offers facilities for lunch and tee/coffee breaks.

• the first week will take place in MDC campus building C81 (FMP) in room 1.14 on the ground floor
• the second week will take place in the library of the MDC campus in building 10 in room 27.1 on the ground floor

see the directions to the MDC campus in Berlin-Buch and a map of the MDC campus.

Contact

In case of general questions including questions regarding the registration for this module, please contact Irmtraud Meyer by email or phone (030-9406-3292). For questions about specific papers, please contact Peter or Stefan directly, see the list of papers.

Background reading

• C.K. Kwok (2016): Dawn of the in vivo RNA structurome and interactome
• J.G. Aw (2016): In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

This seminar will cover central aspects of modern bottom-up proteome analysis by mass spectrometry with a focus on bioinformatic algorithms and data analysis.
    After a brief introduction into the field of mass spectrometry-based proteomics (instrument types, data properties, overview of bioinformatics challenges) we will explore the big cornerstones, including isotope models and averagines, scoring algorithms for the identification of mass spectra, false-discovery-rate estimation using decoy peptides, absolute and relative quantification of proteins and correlation between mRNA and protein expression.

Introductory seminar to computer-aided drug design, including structure- and ligand-based methods. Briefly, computer-aided drug design uses computational chemistry to discover, enhance, or study drugs and related biologically active molecules. In this seminar, the students will independently acquire knowledge about topics in the context of structural bioinformatics. Topics include homology modelling, target assessment, molecular docking, in-silico screening (molecular fingerprints, chemical similarity), ADME and toxicity predictions (QSAR, machine learning), and more.

The students can select a topic from the presented drug development pipeline and (under guidance) will collect material (papers, data and algorithms). At the end of the seminar, they will present the topic as well as an application of such.

It is advisable/helpful (but not mandatory) to attend the practical course ‘Using open source software and libraries for data analysis and computer-aided drug design’ (Volkamer, WiSe 2016/17, block seminar at the end of march) or ‘Current questions of structural bioinformatics’ (Preissner/Banerjee) before.

The set-up of the course will depend on the number of attending students. Preferably, we will have a bi-weekly meeting (half-day) till mid-June, followed by a weekly presentation round (4 dates à 2 hours) till the end of the semester.

More details will be discussed on Thursday, April 26th, 9-11:30 am, Charité, Mitte.

For more information see: AG Volkamer - Teaching

Within this course advance biometrical methods applied within the context of clinical and observational trials are introduced. Issue like complex study designs, sample size (re)calculation and advanced modelling will be addressed among others. Students should have a solid background in statistics and an interest in medical applications of statistics.

Contents:

Introduction: why and where do we need distributed systems? What properties and techniques are important for distributed systems?

Communication in distributed systems: Networks, network services and protocols, classification of communication mechanisms. OS communication services (Pipes, Message Queues, Sockets), communication platforms (PVM, MPI).

Internet network services: remote process invokation, distributed system architectures: Client/Server architecture versus distributed algorithms.

Distributed algorithms: timing and causality, group communication, election algorithms, mutual exclution, consensus.

Distributed data: replication, consistency, caching, distributed storage, object caching, distributed transactions.

Fault-tolerance: terminology, fault classification, replication with voting, consensus, Byzantine agreement.

Distribution transparency: remote calls (Java RMI, .NET Remoting), mobile code, mobile objects, replicated objects, distributed network services (NIS, DNS), Middleware: Sun RPC, COMANDOS, COM/DCOM, CORBA, .NET, WWW, web services, message oriented middleware (IBM MQSeries, CORBA Notification Service, Java Message Service, SIENA).

• Nicola Santoro: Design and Analysis of Distributed Algorithms
• Vijay K Garg: Elements of Distributed Computing.
• A.S. Tanenbaum, M. v.Steen: Distributed Systems.
• G. Coulouris et al.: Distributed Systems - Concepts and Design.
• M. Weber: Verteilte Systeme

Requirement:

basic knowledge in the field of systems software

Content

The lecture is to provide the students with a first structured overview of the German and European Data Protection Law based on the EU General Data Protection Regulation (GDPR). Furthermore, current topics on data protection are being discussed in depth.

Overview of the topics

• Historiy of data protection and privacy
• European and constitutional legal background
• Legislative framework: General Data Protection Regulation, Federal Data Protection Act, sector-specific data protection law
• Basic concepts and scope
• Principles relating to processing of personal data and lawfulness of processing
• Rights of the data subject
• Data protection by design and by default, security of processing, data protection impact assessment
• Enforcement of data protection law: supervisory system, sanctions
• Focal points: big data, profiling, social networks, smart video surveillance, processing in the context of employment

The exact date will be announced.

Content

In a preparatory colloquium, current teaching methods and advising for tutors are presented and discussed. This colloquium is specifically for students, which particularly want to guide exercise sessions as a tutor for the mathematics and computer science students. An interview with the selection committee will take place even during the holidays, in which will be decided about the suitability as a tutor.

After successful aptitude assessment a tutorial about a subjects of a lecture of the first four semesters bachelor study, should be prepare, expose, documented and analyzed.

Seifert, J. W.: Visualisieren Präsentieren Moderieren. GABAL Verlag, 16. Auflage 2001

Time and location by appointment.

Contents

• shell scripting from the viewpoint of system administration
• planning and setting up a computer system while taking availability and maintainability into consideration (RAS-conditions)
• redundancy in networking and storage
• planning and setting up a redundant storage system (Raid-technologies and management)
• system administration, security and user management, accounting and logging
• managing configuration files and documentation
• backups - strategies and technologies
• planning and realization of networkwide services and resources (e.g. file services, print services, network information services)
• implementation on different platforms (AIX, Solaris)
• partitioning, virtualization and resource management on modern systems supporting logical partitioning
• virtualization and resource management at the operating systems level (workload partitions, zones, jails)
• qualitative comparison of partitioning and virtualization techniques on PowerPC and Sparc based UNI*-systems.
• delegation of administration tasks with rolebased access (RBAC)
• ethical and legal aspects when dealing with administrative privileges,
• special aspects and procedures when dealing with personal information and security clearances when dealing with vital systems

At the beginning of the class, we will refresh the necessary knowledge to participate in the practical exercises and we will set up a working environment in the context of the administration of a heterogeneous computer network. Previous experience is desirable.

The class will be taught as a block course, from 26.9. to 14.10.2016, daily from 10:00 to 18:00. Details will be announced in due time.

Contents

• shell scripting from the viewpoint of system administration
• planning and setting up a computer system while taking availability and maintainability into consideration (RAS-conditions)
• redundancy in networking and storage
• planning and setting up a redundant storage system (Raid-technologies and management)
• system administration, security and user management, accounting and logging
• managing configuration files and documentation
• backups - strategies and technologies
• planning and realization of networkwide services and resources (e.g. file services, print services, network information services)
• implementation on different platforms (AIX, Solaris)
• partitioning, virtualization and resource management on modern systems supporting logical partitioning
• virtualization and resource management at the operating systems level (workload partitions, zones, jails)
• qualitative comparison of partitioning and virtualization techniques on PowerPC and Sparc based UNI*-systems.
• delegation of administration tasks with rolebased access (RBAC)
• ethical and legal aspects when dealing with administrative privileges,
• special aspects and procedures when dealing with personal information and security clearances when dealing with vital systems

At the beginning of the class, we will refresh the necessary knowledge to participate in the practical exercises and we will set up a working environment in the context of the administration of a heterogeneous computer network. Previous experience is desirable.

See German version.

See German text version.

Literatur:

Wird in der Vorbesprechung ausgegeben.

See German text version.

Integrative analysis of next generation sequencing (NGS) data
One of the research questions in bioinformatics and regulatory genomics is to understand the principles of transcriptional regulation. Transcription factors are the main players of gene regulation. Another aspect accounts for the open chromatin which enables the binding of the transcription factors and the RNA Polymerase II. There are several experimental techniques which can determine the interaction of the regulatory proteins and the DNA, such as ChIP-seq. Combinatorical analysis of several experiments help us to understand the interplay of all these factors on regulatory elements in the genome. We will analyze ChIP-seq and RNA-seq data in various cell lines to model the TF binding and histone modifications across the genome with respect to gene expression of the neighbouring genes. Afterwards, we develop a statistical method to combine these data in an appropriate way. We will use both implemented tools and our own scripts to obtain suitable results. Students will work in groups of 3 and present their work at the end of the seminar.

See German text version.

The aim of this project is the implementation of algorithms for the analysis of mass spectrometry data within the software library OpenMS. The implemented components will be integrated into complex analysis pipelines of proteomics or metabolomics data within the KNIME workflow system.

Good C++ programming skills are required.

See German text version.

Informationen zum Softwarepraktikum befinden sich auf der Homepage des Studiengangs Bioinformatik.

In diesem Praktikum werden realistische Workflows zur Analyse von biologischen Daten konzeptioniert und implementiert. Die Teilnehmer werden dabei verschiedene Workflowsysteme (KNIME, Snakemake) kennenlernen und verwenden. Die Teilnehmer werden dabei anhand aktueller Literatur ihre Workflows eigenständig erarbeiten, testen und verfeinern. Dabei werden sowohl Kenntnisse im Rahmen der Workflow Programmierung als auch ein Umfangreiches Wissen über existierende Bioinformatik-Software erlangt.

Gute Kenntnisse in Skriptsprachen (Python) sowie R sind Voraussetzung

See German text version.

See German text version.

See German text version.

Platform for ligand-based toxicity prediction

The in silico prediction of compound toxicity is a very important task, i.e. for the reduction of animal testing (http://www.bb3r.de/). In the previous course, we have implement first Python scripts for toxicity predictions using machine learning and similarity searches and we have developed a prototype of a webserver.

In this year’s project, we will continue working on the scripts and include other machine learning algorithms, different molecular descriptors as well as more data sets. Besides exhaustive evaluation of the models, the webservice will be enhanced in features and usability.

The goal is to make the web-server freely available to allow other researchers to predict the toxicity of their compound of interest. A potential publication would be desirable.

Used programming languages: Python (scikit-learn, RDKit), Webserver (django, json, jquery, …)

For further information on the research interests of the group see https://physiologie-ccm.charite.de/en/research_at_the_institute/team_volkamer/

See German text version.

See German text version.

See German text version.

Content

The lecture is to provide the students with a first structured overview of the German and European Data Protection Law based on the EU General Data Protection Regulation (GDPR). Furthermore, current topics on data protection are being discussed in depth.

Overview of the topics

• Historiy of data protection and privacy
• European and constitutional legal background
• Legislative framework: General Data Protection Regulation, Federal Data Protection Act, sector-specific data protection law
• Basic concepts and scope
• Principles relating to processing of personal data and lawfulness of processing
• Rights of the data subject
• Data protection by design and by default, security of processing, data protection impact assessment
• Enforcement of data protection law: supervisory system, sanctions
• Focal points: big data, profiling, social networks, smart video surveillance, processing in the context of employment

The exact date will be announced.

Content

In a preparatory colloquium, current teaching methods and advising for tutors are presented and discussed. This colloquium is specifically for students, which particularly want to guide exercise sessions as a tutor for the mathematics and computer science students. An interview with the selection committee will take place even during the holidays, in which will be decided about the suitability as a tutor.

After successful aptitude assessment a tutorial about a subjects of a lecture of the first four semesters bachelor study, should be prepare, expose, documented and analyzed.

Seifert, J. W.: Visualisieren Präsentieren Moderieren. GABAL Verlag, 16. Auflage 2001

Time and location by appointment.

Contents

• shell scripting from the viewpoint of system administration
• planning and setting up a computer system while taking availability and maintainability into consideration (RAS-conditions)
• redundancy in networking and storage
• planning and setting up a redundant storage system (Raid-technologies and management)
• system administration, security and user management, accounting and logging
• managing configuration files and documentation
• backups - strategies and technologies
• planning and realization of networkwide services and resources (e.g. file services, print services, network information services)
• implementation on different platforms (AIX, Solaris)
• partitioning, virtualization and resource management on modern systems supporting logical partitioning
• virtualization and resource management at the operating systems level (workload partitions, zones, jails)
• qualitative comparison of partitioning and virtualization techniques on PowerPC and Sparc based UNI*-systems.
• delegation of administration tasks with rolebased access (RBAC)
• ethical and legal aspects when dealing with administrative privileges,
• special aspects and procedures when dealing with personal information and security clearances when dealing with vital systems

At the beginning of the class, we will refresh the necessary knowledge to participate in the practical exercises and we will set up a working environment in the context of the administration of a heterogeneous computer network. Previous experience is desirable.

The class will be taught as a block course, from 26.9. to 14.10.2016, daily from 10:00 to 18:00. Details will be announced in due time.

Contents

• shell scripting from the viewpoint of system administration
• planning and setting up a computer system while taking availability and maintainability into consideration (RAS-conditions)
• redundancy in networking and storage
• planning and setting up a redundant storage system (Raid-technologies and management)
• system administration, security and user management, accounting and logging
• managing configuration files and documentation
• backups - strategies and technologies
• planning and realization of networkwide services and resources (e.g. file services, print services, network information services)
• implementation on different platforms (AIX, Solaris)
• partitioning, virtualization and resource management on modern systems supporting logical partitioning
• virtualization and resource management at the operating systems level (workload partitions, zones, jails)
• qualitative comparison of partitioning and virtualization techniques on PowerPC and Sparc based UNI*-systems.
• delegation of administration tasks with rolebased access (RBAC)
• ethical and legal aspects when dealing with administrative privileges,
• special aspects and procedures when dealing with personal information and security clearances when dealing with vital systems

At the beginning of the class, we will refresh the necessary knowledge to participate in the practical exercises and we will set up a working environment in the context of the administration of a heterogeneous computer network. Previous experience is desirable.

For further information see german text version.

This course offers information and support for all incoming exchange students and regular students from foreign countries in the department of mathematics and computer science. Feel free to join our course in the KVV or visit our web pages.

All information sessions are voluntary, there is no compulsory attendance. Topics and dates of all information sessions can be changed according to your needs. Don't hesitate asking and suggesting topics you are interested in!