August 2016 - BBClist - maillist.psb.ugent.be

[Gtpb] GTPB Bioinformatics Training course REMINDER - AET16 - Applied Evolutionary Theory
by Pedro Fernandes 16 Aug '16

16 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course AET16 - Applied Evolutionary Theory with Claudia Bank, Rafael Guerrero and Stephan Peischl are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/AET16 for details. IMPORTANT DATES for this Course Deadline for applications: Oct 25th 2016 Course dates: Nov 7th - Nov 11th 2016 Course Description For many of its history, our knowledge of evolution has been based heavily on theoretical models and hypotheses. In the age of novel experimental and technological approaches, we are now increasingly able to evaluate this theory; however, the basics of how and why to develop and analyse a simple model are often forgotten in the process of NGS analysis. This course aims at training evolutionary biologists in classical modelling and teach them ways to approach their own research questions through evolutionary theory. Primarily through interactive hands-on sessions, complemented by an introduction to the cornerstones of modelling and its application to data analysis, this course will familiarize the participants with ways of approaching a research question with a simple model, and different strategies at gaining insight from the model. In groups of two, course participants will develop and analyse their own toy model in the course and present their findings to the group on the last day. Topics that will be covered in the course include the following: Why and how are models useful? How to write down/develop a model How simple/complicated should a model be? Which modelling approach/programming language should I use for my question? How to nail down a question with a model Extracting results from an equation/simulation How to evaluate a model using empirical data Participants can use their preferred programming language during the hands-on sessions, and free access to Wolfram Mathematica will be provided. The instructors have modelling experience using Mathematica, R, Python, and C++. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] GTPB Bioinformatics Training course REMINDER - 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding
by Pedro Fernandes 16 Aug '16

16 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding are open. with Marc Marti-Renom, François Serra and Davide Baù IMPORTANT DATES for this Course Deadline for applications: September 30th 2016 Notification of acceptance within 72 hours of application (working days count) Course date: Oct 10th to Oct 14th 2016 Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/3DAROC16 for details. Course Description 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in the space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html ). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Analyze and compare different samples. Participants can bring- specific biological questions and/or their own 3C-based data to analyse during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyse Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] GTPB Bioinformatics Training course REMINDER - Precision Medicine - PM16
by Pedro Fernandes 16 Aug '16

16 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course PM16 - Precision Medicine with Fatima Al-Shahrour, Javier Perales and Elena Piñero are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/PM16 for details. Course Description The implementation of cancer genomics into the clinic is becoming a reality. Personalised medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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ECCB 2016: online registration deadline August 19!
by Femke Francissen 16 Aug '16

16 Aug '16

Dear colleagues, The online registration deadline for the ECCB 2016 is August 19, 2016! Don't hesitate and join us for the 15th European Conference on Computational Biology from 3-7 September 2016 in The Hague in The Netherlands. Register via: http://www.eccb2016.org/registration/ We have composed an exciting programme with workshops/tutorials, keynote speakers, highlight talks, proceeding talks, application talks, poster sessions, an ELIXIR track, and a very nice social programme (conference dinner, opening reception, morning run, yoga sessions, The Hague at night). You can find all the relevant information on the conference website: http://www.eccb2016.org *-------------------------------------------------------------------------------------------------------* *15th European Conference on Computational Biology (ECCB 2016)* *3-7 September 2016* World Forum Convention Center The Hague, The Netherlands Website: http://www.eccb2016.org/ ------------------------------------------------------------ ------------------------------------------- ** ** *Organisers* The conference is hosted by: BioSB research school <http://www.biosb.nl/>, Dutch Techcentre for Life Sciences <http://www.dtls.nl/> and co-organised by: Vrije Universiteit Amsterdam, Delft University of Technology Contact: info(a)eccb2016.org

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'PYTHON (introductory) course'
by Oliver Hooker 16 Aug '16

16 Aug '16

INTRODUCTION TO PYTHON FOR BIOLOGISTS This course is being delivered by Dr Martin Jones, an expert in Python and author of two text books, Python for Biologists [http://www.amazon.com/Python-Biologists-complete-programming-beginners/dp/1…] Advanced Python for Biologists [http://www.amazon.com/Advanced-Python-Biologists-Martin-Jones/dp/1495244377/] This course will run from 3rd - 7th October 2016 at Malham Tarn field station, Yorkshire dales national park, England. http://prstatistics.com/course/introduction-to-python-for-biologists-ipyb-3/ Course overview: Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackle problems in their own research and (2) continue their Python education in a self-directed way. Curriculum: Day 1: Module 1 - Introduction Module 2 - Output and text manipulation Day 2: Module 3 - File IO and user interfaces Module 4 - Flow control 1: loops Day 3: Module 5 - Flow control 2: conditionals Module 6 - Organizing and structuring code Day 4: Module 7 – Regular expressions Module 8 - Dictionaries Day 5: Module 9 – Interaction with the file system Module 10 - Optional free afternoon to cover previous modules and discuss data more details at http://prstatistics.com/course/introduction-to-python-for-biologists-ipyb/ Intended audience: This workshop is aimed at all researchers and technical workers with a background in biology who want to learn programming. The syllabus has been planned with complete beginners in mind; people with previous programming experience are welcome to attend as a refresher but may find the pace a bit slow. Teaching format: The workshop is delivered over ten half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organizer’s discretion. There will also be plenty of time for students to discuss their own problems and data. Assumed background: Students should have enough biological background to appreciate the examples and exercise problems (i.e. they should know about DNA and protein sequences, what translation is, and what introns and exons are). No previous programming experience or computer skills (beyond the ability to use a text editor) are necessary, but you'll need to have a laptop with Python installed. The cost is £530 (+VAT) including lunches and course materials. An all-inclusive option is also available at £660 (+VAT); this includes breakfast, lunch, dinner, refreshments, accommodation and course materials. Participants will need a laptop with a recent version of Python installed. Please send inquiries to oliverhooker(a)prstatistics.co.uk or visit the website www.prstatistics.com Please fee free to distribute this information anywhere you think suitable Other upcoming courses - 1. INTRODUCTION TO BIOINFORMATICS USING LINUX (August) 2. GENETIC DATA ANALYSIS / EXPLORATION USING R (August) 3. INTRODUCTION TO BAYESIAN HIERARCHICAL MODELLING (August) 4. INTRODUCTION TO PYTHON FOR BIOLOGISTS (October) 5. LANDSCAPE (POPULATION) GENETIC DATA ANALYSIS USING R (October) 6. APPLIED BAYESIAN MODELLING FOR ECOLOGISTS AND EPIDEMIOLOGISTS (October) 7. SPATIAL ANALYSIS OF ECOLOGIC AL DATA USING R (November) 8. ADVANCING IN STATISTICAL MODELLING USING R (December) 9. MODEL BASED MULTIVARIATE ANALYSIS OF ECOLOGICAL DATA USING R (January) 10. ADVACNED PYTHON FOR BIOLOGISTS (February) 11. NETWORK ANALYSIS FOR ECOLOGISTS (March) 12. INTRODUCTION TO GEOMETRIC MORPHOMETRICS USING R (June) Oliver Hooker PR statistics 3/1 128 Brunswick Street Glasgow G1 1TF +44 (0) 7966500340 www.prstatistics.com www.prstatistics.com/organiser/oliver-hooker/

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[Gtpb] GTPB Bioinformatics Training course announcement/reminder - 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding
by Pedro Fernandes 12 Aug '16

12 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding are open. with Marc Marti-Renom, François Serra and Davide Baù IMPORTANT DATES for this Course Deadline for applications: September 30th 2016 Notification of acceptance within 72 hours of application (working days count) Course date: Oct 10th to Oct 14th 2016 Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/3DAROC16 for details. Course Description 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in the space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html ). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Analyze and compare different samples. Participants can bring- specific biological questions and/or their own 3C-based data to analyse during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyse Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] GTPB Bioinformatics Training course announcement/reminder - AET16 - Applied Evolutionary Theory
by Pedro Fernandes 12 Aug '16

12 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course AET16 - Applied Evolutionary Theory with Claudia Bank, Rafael Guerrero and Stephan Peischl are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/AET16 for details. IMPORTANT DATES for this Course Deadline for applications: Oct 25th 2016 Course dates: Nov 7th - Nov 11th 2016 Course Description For many of its history, our knowledge of evolution has been based heavily on theoretical models and hypotheses. In the age of novel experimental and technological approaches, we are now increasingly able to evaluate this theory; however, the basics of how and why to develop and analyse a simple model are often forgotten in the process of NGS analysis. This course aims at training evolutionary biologists in classical modelling and teach them ways to approach their own research questions through evolutionary theory. Primarily through interactive hands-on sessions, complemented by an introduction to the cornerstones of modelling and its application to data analysis, this course will familiarize the participants with ways of approaching a research question with a simple model, and different strategies at gaining insight from the model. In groups of two, course participants will develop and analyse their own toy model in the course and present their findings to the group on the last day. Topics that will be covered in the course include the following: Why and how are models useful? How to write down/develop a model How simple/complicated should a model be? Which modelling approach/programming language should I use for my question? How to nail down a question with a model Extracting results from an equation/simulation How to evaluate a model using empirical data Participants can use their preferred programming language during the hands-on sessions, and free access to Wolfram Mathematica will be provided. The instructors have modelling experience using Mathematica, R, Python, and C++. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] GTPB Bioinformatics Training course announcement/reminder - Precision Medicine - PM16
by Pedro Fernandes 12 Aug '16

12 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course PM16 - Precision Medicine with Fatima Al-Shahrour, Javier Perales and Elena Piñero are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/PM16 for details. Course Description The implementation of cancer genomics into the clinic is becoming a reality. Personalized medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Posting assistant professor position on BBC mailing list
by Marcel Reinders - EWI 10 Aug '16

10 Aug '16

Dear BBC list owner, I would like to post the attached message on the BBC mailing list. Is that possible? Best regards, Marcel Reinders.

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VIB BITS Training courses September 2016
by Alexander Botzki 10 Aug '16

10 Aug '16

Dear all, For your information, please find below our offering of training courses for September 2016. Basic statistics in R This training gives an introduction to the use of the statistical software language R. This introduction is aimed at beginners. The training covers data handling, graphics, mathematical functions and some basic statistical techniques. Requirements Understanding of basic statistical concepts is required, such as data types, normal distribution, descriptive statistics, tests for comparing groups... If you want to follow the metagenomics training or the RNA-Seq training and you have no experience in R, you are strongly encouraged to follow this introduction. Date: 2 and 9 September Location: Park Inn, Leuven Trainer: Janick Mathys More information and registration: http://www.vib.be/en/training/research-training/courses/Pages/default.aspx?… Mass spectrometry data processing In this training we start by reviewing the types of mass spectrometers, and what the properties of their output data are. Out of our understanding of the data, we learn to extract meaningful interpretations. Requirements: basic understanding of mass spectrometry as applied to peptides and proteins. Date: 12 and 13 September Location: BioAccelerator, Gent Trainer: Lennart Martens More information and registration: http://www.vib.be/en/training/research-training/courses/Pages/default.aspx?… Metagenomics This training will start with the presentation of a 16S pipeline in a Linux environment, using a minimal amount of Linux commands. This will enable the preprocessing of the data going from raw reads to taxonomic tables and phylogenetic trees. The second part of the training will give an overview of numerical ecology and takes part in R. Requirements: The training is intended for people who have some experience with R. If you have no experience with R you can attend the R introduction training. Linux usage will be part of the course, but very basic Linux knowledge is sufficient for this course. Date: 16 September Location: Park Inn, Leuven Trainer: Falk Hildebrand More information and registration: http://www.vib.be/en/training/research-training/courses/Pages/default.aspx?… Linux for bioinformatics This hands-on training will show you how to effectively use Linux,, be it on the server of your department, or on your own computer (even if you're already running Windows or Mac OS). Date: 23 and 26 September Location: Park Inn, Leuven Trainer: Christof De Bo More information and registration: http://www.vib.be/en/training/research-training/courses/Pages/default.aspx?… Best regards, Alex Alexander Botzki Manager BITS | Training Coordinator ELIXIR-BE VIB - BITS, Rijvisschestraat 126, 9052 GENT | +32 9 248 16 00 www.bits.vib.be | @bitsatvib | https://corefacilities.vib.be

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