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BIOINFORMATICS TRAINING

BIOINFORMATICS TRAININGBIOINFORMATICS TRAINING

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01/02/2018 to 07/05/2018
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BIOINFORMATICS TRAINING

Bioinformatics Room (468)

The CRG Bioinformatics training will consists of 5 courses spread from February to May 2018 to give a basic knowledge on bioinformatics. These courses are not completely linked therefore you can register to those that you need the most. However, please double check the requisites for each course.

CRG Bioinformatics Training

Courses

Basic Bioinformatic Course

Description

This course will allow any CRG student to perform basic bioinformatics and use the most common tools for their projects. Each topic includes 1-4 short assignments (15’ videos or short readings) that the students must undertake during the week before the actual session (of 1h) on Fridays. During the interactive session, the teachers answers questions and explains the next topic.

Trainers

Eduard Sabidó & Toni Hermoso

Topics, date, time & location

Module Date Hour Location Title
T01 01/02/2018 12:00-13:00 Bioinformatics room (468) Introduction to bioinformatics and data science
T02 09/02/2018 11:00-12:00 Bioinformatics room (468) Setting up and managing a bioinformatics project
T03 16/02/2018 11:00-12:00 Bioinformatics room (468) Interacting with machines I: Unix systems
T04 23/02/2018 11:00-12:00 Bioinformatics room (468) Interacting with machines II: Data formats
T05 01/03/2018 11:00-12:00 Bioinformatics room (468) Introduction to basic programming
T06 09/03/2018 11:00-12:00 Bioinformatics room (468) Bioinformatics resources and databases
T07 16/03/2018 11:00-12:00 Bioinformatics room (468) Multiple sequence alignment, similarity searches, and pattern recognition
T08 23/03/2018 11:00-12:00 Bioinformatics room (468) Genome Assembly and ChIP-Seq
T09 06/04/2018 11:00-12:00 Bioinformatics room (468) Proteomics analyses
T10 13/04/2018 11:00-12:00 Bioinformatics room (468) Integrative platforms: Galaxy

Linux Course

Description

This course is suitable for beginners and explains the basics of GNU/Linux commands and scripts creation.

Trainer

Rodny Hernández

Topics

  • Introduction (Linux OS and distributions)
  • User accounts
  • Secure shell (access to remote servers)
  • Man pages
  • Working with files and directories (Linux file tree)
  • Basic Linux commands: (ls, cp, mkdir, rm, mv, find, man, grep, cut, sort...)
  • Files permissions (groups, files, chown, chmod)
  • Pipes and redirections
  • Editor (gedit)
  • Script creation (conditional structures, loops)

Date, time & location

5th March 2018 10:00-13:00 / Bioinformatics Room (468)

Cluster Usage Course

Description

The course is an introduction to the CRG's computing cluster usage and encompass the following key concepts:

Trainer

Gabriel González

Topics

  • Univa Grid Engine Introduction
  • Cluster concepts (jobs, queues, nodes, slots, memory)
  • Cluster information (qstat, qhost)
  • Submitting jobs to the cluster (qsub CLI)
  • Managing submitted jobs (qstat, qhold, qdel)
  • Submit script requesting basic parameters (memory, number of slots)
  • Intermediate data and output management (-e, -o and scratch usage for improving jobs performance)
  • Job arrays

Date, time & location

6th March 2018 10:00-13:00 / Bioinformatics Room (468)

Requisites

In order to attend the Cluster Usage Workshop user should already be familiar with Linux environment.

Introduction to R

Description

This is an introductory course to R programming. The R part is offered in 4 classes for absolute beginners. For practical exercises we will use R programming language and R Studio.

Trainer

Sarah Bonnin

Topics

  • Introduction to R studio.
  • Simple arithmetic in R console.
  • Objects, data types and data structures.
  • Create and run a short script.
  • Read and write a file.
  • Packages.
  • Basic plotting and introduction to ggplot2 package.
  • TBC

Date, time & location

19th & 20th March 2018 10:00-14:00 / Bioinformatics Room (468)

16th & 17th April 2018 10:00-14:00 / Bioinformatics Room (468)

Requisites

Soon a new Biostatistics training will start and to be able to enroll you need a basic knowledge on R. Therefore, we advise that if you want to enroll in the coming biostatistics training you should register to Introduction to R unless you already have some basic knowledge.

Bioinformatics best practices

Description

This course will go through some good practices in bioinformatics and in computer science in general regarding storage, files / directories organization, text editors etc.

Trainer

Sarah Bonnin

Topics

TBC

Date, time & location

7th May 2018 10:00-14:00 / Bioinformatics Room (468)

Coming soon

Soon we will announce the Biostatistics training that will start on the 20th April till 22nd of June, to register to this courses you need a basic knowledge on R. Therefore, we advise you that if you want to enroll to this coming training, you register to Introduction to R.

Registration

To register to any of these courses, click HERE. To fill this form you will need to log in.

After the deadline we will confirm if you have been accepted to the training(s). Please, make sure to check your calendar, if there is a cancelation without justification this will penalize for future internal trainings.  

Contact

For any further question contact:

Training Unit – training@crg.eu

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