Focus on:  Hide Contributions
Europe/Brussels English Login

CANCELLED! Introduction to scientific computing

→ Europe/Brussels
Description

Course presentation

Summary

The modern world is ever more dependent on computer science and information technology advances. Especially in life science in recent years, exponentially growing amounts of biological information have been obtained and deposited in various databases. The predominant source – but not only – of this data is “high-throughput” experimentation, involving simultaneous execution of hundreds or thousands of experiments. A comprehensive understanding of biological phenomena can be achieved only through the integration of all available biological information and different data analysis tools and applications. It becomes crucial for modern scientists to acquire skills that will enable them to efficiently deal with this “data explosion”. It is not surprising that scientists with strong computer skills fare better in their position and research. This course aims to provide learners with the basic notions underlying computer science as necessary for biomedical science. The focus of this course in on computer architecture, scientific computing and basic programming.

Aim of the course

To provide participants with basic knowledge on computer architecture, available storage and computing resources, good IT practices, and some programming skills in Python.

By the end of the course, the participants should:

  • understand personal computer & cluster architecture along with mass-storage, and their usage;
  • be acquainted with the available IT resources and people in charge at the GIGA/ULiège IT infrastructure;
  • be aware of some principles of good programming practice;
  • know about the main operational systems & programming languages;
  • write basic scripts and functions in Python.

Python programming

This module of 5 x 3h trainings will teach you the basics of Python scripting. At the end of the formation you will be able to write simple scripts and be familiar with the Python syntax, data types, flow control, file input/output and error catching. This won't make you a Python expert in the blink of an eye but rather give you the tools to start your Pythonista journey and be able to grow independently.

No particular pre-requisite is required. Although it is quite possible to follow the courses in a passive way, it is much better to bring your own laptop to interact and practice live.

The material for the Python course can be found here. This introduction will cover the 5 basics courses.

Practicalities

Target group

PhD candidate, postdoctoral researchers and PI’s. 
Course is limited to 14 participants.

Duration of the course and location

5 days split between the GIGA+5 and CRC (B30):

  • November 21st, B34/+5, GIGA - Auditoire Léon Fredericq
  • November 28th, B30, CRC - Big meeting room
  • December 5th, B34/+5, GIGA - Grande Ghuysen
  • December 12th, B34/+5, GIGA - Auditoire Léon Fredericq
  • December 19th, B34/+5, GIGA - Grande Ghuysen

In total, 30 hours.

Prerequisites

For the practical and programming sessions:

For GIGA members, the bioinformatics team wiki provides practical information about the mass-storage and cluster, including good practice recommendation and how to connect. Do not hesitate to contact them if you don't have access or are not sure you have access to the GIGA mass storage.

IT requirements: at the very least make sure you have your 'u' or 's' account (preferably the former)

Organization of the course

The course is a mixture of in-person theoretical lectures, live demonstrations and practical sessions:

  • 5 days, over the course of 5 weeks, for in-person teaching with
    • in the morning, lectures, demo and hands-on;
    • in the afternoon, python basics.
  • the remaining 3 weeks, with on line programming courses and exercises to solve, plus extra-lectures on topics covered in-person (when available).

Some of the lectures were recorded in October 2020 and are available here.

Speakers & Contributors

in alphabetical order:

Support resources

Additional resources & extra lectures

Python online courses:

Scientific computing, IT & Linux:

Reproducibility & reliability, QA & QC in software, and Open Source Software

Git, GitHub, Gitlab

 

  • Tuesday, 21 November
    • 09:30 → 10:00
      Welcome + Introduction to computer science : historical perspective, computer structure, operating systems & languages 30m B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)
    • 10:00 → 11:00
      Data representation & storage: bits/bytes, data format, signal discretization, compression 1h B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: Dr Mohamed Bahri
    • 11:00 → 11:30
      Coffee break 30m
    • 11:30 → 12:00
      GIGA-ULiege Mass storage 30m B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: David Stern
    • 12:00 → 13:30
      Lunch break 1h 30m
    • 13:30 → 16:30
      Python basics 1: Introduction + tools 3h B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130

      https://gitlab.uliege.be/giga-bioinfo/trainings/python_course/-/tree/master/1-Basics

      Speaker: Olivier Renson (ULiege)
      Python, the basics
    • 16:30 → 17:00
      (ULiège IT resources by the SeGI/UDI’s) TBC. 30m B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: Mr Yves Wesche
  • Tuesday, 28 November
    • 09:00 → 10:00
      Research Data Management and Reproducibility: good habits for good research 1h B-30/0-000 - Big meeting room (CRC)

      B-30/0-000 - Big meeting room

      CRC

      20
      Speaker: Dr Judith Biernaux (ARD ULiege)
    • 10:00 → 11:00
      Working with personal data ? Think GDPR! 1h B-30/0-000 - Big meeting room (CRC)

      B-30/0-000 - Big meeting room

      CRC

      20
      Speaker: Mr Pierre-François Pirlet
    • 11:00 → 11:30
      Coffee break 30m
    • 11:30 → 12:30
      Data processing in genomics, from the sequencers to the results: data management, pipelines and containers, reproductibility. 1h B-30/0-000 - Big meeting room (CRC)

      B-30/0-000 - Big meeting room

      CRC

      20
      Speaker: Dr Arnaud Lavergne
    • 12:30 → 13:30
      Lunch break 1h
    • 13:30 → 16:30
      Python basics 2: Operators, variables, conditions and loops 3h B-30/0-000 - Big meeting room (CRC)

      B-30/0-000 - Big meeting room

      CRC

      20

      https://gitlab.uliege.be/giga-bioinfo/trainings/python_course/-/tree/master/1-Basics

      Speaker: Olivier Renson (ULiege)
      Python, the basics
  • Tuesday, 5 December
    • 09:00 → 10:00
      Introduction to algorithmic thinking: Different types of algorithms, computer logic. 1h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speaker: Dr Mohamed Bahri
    • 10:00 → 11:00
      Good practices in scientific computing: Code modularity, validation, optimization, documentation 1h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)
    • 11:00 → 11:30
      Coffee break 30m
    • 11:30 → 12:30
      Working with High Performance Computing Clusters & parallel processing. 1h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speaker: Dr Alice Mayer
    • 12:30 → 13:30
      Lunch break 1h
    • 13:30 → 16:30
      Python basics 3: Data structures 3h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25

      https://gitlab.uliege.be/giga-bioinfo/trainings/python_course/-/tree/master/1-Basics

      Speaker: Olivier Renson (ULiege)
      Python, the basics
  • Tuesday, 12 December
    • 09:00 → 09:45
      Code versioning & Git, an introduction. 45m B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)
    • 09:45 → 10:45
      GitHub/Gitlab account hands-on check and explanations (1/2) 1h B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: Dr Grégory Hammad (GIGA-CRC in vivo imaging)
    • 10:45 → 11:15
      Coffee break 30m
    • 11:15 → 12:00
      GitHub/Gitlab account hands-on check and explanations (2/2) 45m B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130
      Speaker: Dr Grégory Hammad (GIGA-CRC in vivo imaging)
    • 12:00 → 13:30
      Lunch break 1h 30m
    • 13:30 → 16:30
      Python basics 4: Functions and Errors Catching 3h B34/+5-59a - Auditoire Léon Fredericq (GIGA meeting rooms)

      B34/+5-59a - Auditoire Léon Fredericq

      GIGA meeting rooms

      130

      https://gitlab.uliege.be/giga-bioinfo/trainings/python_course/-/tree/master/1-Basics

      Speaker: Olivier Renson (ULiege)
      Python, the basics
  • Tuesday, 19 December
    • 09:00 → 10:00
      Introduction to AI 1h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speaker: Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)
    • 10:00 → 11:00
      AI demo 1h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speaker: Alexandre Hego
    • 11:00 → 11:30
      Coffee break 30m
    • 11:30 → 12:30
      Access to and use of the mass storage 1h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speaker: Dr Alice Mayer
    • 12:30 → 13:30
      Lunch break 1h
    • 13:30 → 16:30
      Python basics 5: File I/O, os interaction and exercises 3h B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25

      https://gitlab.uliege.be/giga-bioinfo/trainings/python_course/-/tree/master/1-Basics

      Speaker: Olivier Renson (ULiege)
      Python, the basics
    • 16:30 → 16:45
      Closing comments + Q&A 15m B34/+5-42 - Grande Ghuysen (GIGA meeting rooms)

      B34/+5-42 - Grande Ghuysen

      GIGA meeting rooms

      25
      Speakers: Dr Alice Mayer, Prof. Christophe Phillips (GIGA in silico medicine & CRC in vivo imaging)
Powered by Indico v2.3.5