[BBC] Upcoming BioSB courses: Machine Learning, Algorithms for Genomics, Constraint-based modelling

[Femke Francissen]

Dear colleague,

Registration is open for the following courses of the BioSB research school
<http://www.biosb.nl> (more detailed information below):

   - Machine Learning for bioinformatics and systems biology
   <https://www.biosb.nl/archive-courses/machine-learning-for-bioinformatics-systems-biology/>
   - 7-11 October 2019, Delft/Amsterdam, the Netherlands
   - Algorithms for Genomics
   <https://www.biosb.nl/archive-courses/course-algorithms-for-genomics/> -
   14-18 October 2019, Delft, the Netherlands
   - Constraint-based modelling
   <https://www.biosb.nl/archive-courses/constraint-based-modelling-introduction-and-advanced-topics-2019/>
   - 25-29 November 2019, Leiden, the Netherlands

*** Machine Learning for bioinformatics and systems biology, 7-11 October
2019, Delft/Amsterdam, the Netherlands*

Modern biology is a data-rich science, driven by our ability to measure the
detailed molecular characteristics of cells, organs, and individuals at
many different levels. Interpretation of these large-scale biological data
requires the detection of statistical dependencies and patterns in order to
establish useful models of complex biological systems. Techniques from
machine learning are key in this endeavour. Typical examples are the
visualization of single-cell RNA-seq data using dimensionality reduction
methods, base calling for nanopore sequencing data using hidden Markov
models and (recurrent) neural networks, and classification of
high-throughput microscopy image data using convolutional neural networks.

In this one-week course, the foundations of machine learning will be laid
out and commonly used methods for unsupervised (clustering, dimensionality
reduction, visualization) and supervised (mainly classification) learning
will be explained in detail. Methods will be illustrated using recent
examples from the fields of systems biology and bioinformatics. Methods
discussed in the morning lectures will be put into practice during the
afternoon computer lab sessions.

Read more & register
<https://www.biosb.nl/archive-courses/machine-learning-for-bioinformatics-systems-biology/>


*** Algorithms for Genomics, 14-18 October 2019, Delft, the Netherlands*
Comparative genomics aims to compare large sets of genomes in order to
understand and explain differences in traits of an organism. Contemporary
methods are powered by fundamental algorithms and data structures, which
are efficient and scale to large data sets. A thorough understanding of
these algorithms and data structures is necessary for advanced users and
developers in this area. In addition, understanding how comparative
genomics is developing is important to shape your own research.

In this 5-day course, we will cover genome analysis, variant analysis, and
pangenomics. Core concepts, applications, and future trends will be
discussed, with a focus on the algorithms and data structures underlying
state-of-the-art methods. The course offers an engaging mix of lectures,
paper discussions, hands-on tutorials, and a do-it-yourself project.

Read more & register
<https://www.biosb.nl/archive-courses/course-algorithms-for-genomics/>


*** Constraint-based modelling: Introduction & advanced topics, 25-29
November 2019, Leiden, the Netherlands*
Constraint-based modeling is a powerful modeling methodology that is being
used to model a diverse range of biological phenomena. These include both
fundamental and applied questions relevant to biotechnology, microbiology
and medicine. Central to constraint-based modeling is the use of
genome-scale reconstructions that represent particular cellular functions
as a biochemical reaction network. In this 5-day course, you will be
introduced to:

   - the principles of constraint-based reconstruction and analysis (COBRA)
   - the underlying mathematical foundations of constraint-based modeling
   - methods for integration of omics data with constraint-based models
   - basic and advanced methods for interrogating models and interpreting
   results
   - open source COBRA software, including the COBRA Toolbox
   - standards for reconstruction and model sharing
   - example applications to biomedicine and biotechnology

The course is structured into both lectures and practical sessions so that
theory can be illustrated with biologically motivated computational
examples.

Read more & register
<https://www.biosb.nl/archive-courses/constraint-based-modelling-introduction-and-advanced-topics-2019/>

These courses are part of the BioSB research school course portfolio
<https://www.biosb.nl/education/course-portfolio/>. The BioSB research
school offers a wide variety of training courses that enable life
scientists to apply modelling and computational approaches in addressing
scientific challenges.

Best regards,

Femke Francissen

*Femke Francissen*
Community manager
BioSB Research School
*V*isiting address: Jaarbeurs Innovation Mile (JIM) | 6th floor
Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht
E-mail: femke.francissen at biosb.nl
Website: www.biosb.nl
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