Courses

“Image segmentation and analysis course”

This course will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

• - On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based around Fiji, an extensible open source software package.
• - On day 2 we will focus on machine learning and computer vision for the analysis of images in cell biology. We will introduce the methodology in a series of lectures and show their application in the hands-on session. These practical sessions will be based on CellCognition, a tool for the analysis of live cell imaging data.
• - On day 3 we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager)..

Open for registration at http://training.csx.cam.ac.uk/bioinformatics/event/1544771

“Image segmentation and analysis course”

Organized by Gabriela Rustici (EMBL-EBI) and Rafael Carazo Salas (University of Cambridge) will take place 22-23rd of April, 2015.

This course will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

• - On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based around Fiji, an extensible open source software package.
• - On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.
• - On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.

Open for registration at http://training.csx.cam.ac.uk/event/1372458

WiSoft^® Software Use and Platform Programming Advanced Course

The course (webinar) is organized by IDEA-Bio Medical, in 2015, February 23-24.

Application deadline is 12^th of February. Please fill in the registration form and send it to yael-p@idea-bio.com

For more information please contact Dr. Yael Paran,  yael-p@idea-bio.com 

EMBO Practical Course

High Throughput Microscopy for Systems Biology

Modeling-Course: "Modeling Cellular Processes in Space and Time"

October 5--11, 2014   Porquerolles, France

This course is focused on mathematical modeling of biological systems. It is designed for    PhD students and postdocs from biology with a strong interest for modeling and students from a physics/mathematics background willing to enter the field of biology. The course will cover standard modern methods to model the living cell, and will introduce the students to advanced computational tools, like Cytosim (http://www.cytosim.org) or Smoldyn (http://www.smoldyn.org).

Topics covered by the course will range from fundamental stochastic processes, like reactions in simple biological networks and stochastic motions of molecular motors (on cytoskeletal filaments), to coarse-grained mathematical descriptions of cytoskeletal mechanics by partial-differential equations. Students will build simulations with the help of instructors, starting from basic building blocks, and learn efficiently use of computing resources. Students will also be encouraged to propose topics based on a problem of their choice.

For more info, please visit: http://www.embl.de/external/events/2014/MOD14

CSAMA 2014: Computational Statistics for Genome Biology (12^th edition)

Bressanone-Brixen, June 22^rd - June 27^th, 2014

For more info: http://www-huber.embl.de/csama

CSAMA 2013: Computational Statistics for Genome Biology (11th edition)

This one-week intensive course teaches current approaches in statistical and computational analysis of large-scale experiments in biology. The course focus on the methods for downstream analysis of high-throughput sequencing experiments, including DNA sequencing (variant calling), RNA sequencing (differential expression), QTL analysis, epigenetics. Lectures also cover basics including statistical testing, machine learning and bioinformatic metadata integration.

For more info: http://marray.economia.unimi.it/2013/