Welcome to the Amsterdam Science Park Study Group!
Let's work together to speed up research
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Activities

Amsterdam Science Park Study Group is dedicated to building a community of computational biologists and bioinformaticians. This Study Group promotes skill sharing and collaboration by (1) organizing interactive coding workshops, (2) regularly organise co-working sessions for peer-to-peer assistance, (4) act as local hub of the Software/Data Carpentry Foundation and, (4) bring researchers together at social events (e.g. hackatons). All are welcome to this study group, regardless of scientific research area, affiliation or training level.
We use Slack to discuss and ask for help on data and code-related topics. Click on Contact and select Join Slack. You will need to create an account with a username, and log in to read and post. You can use Slack right from a web browser, or you can download a standalone Slack application to your Mac, Windows, Linux and/or Android/iOS device. You can control whether you receive notifications on new posts by going to Preferences, as well as decide which ‘channels’ to subscribe to. A ‘channel’ is a discussion thread, which is used to organize communications into topics. Several channels have been set up for specific topics (R, metagenomics, etc.)
All are welcome! Regardless of scientific research area, affiliation or programming level (absolute beginner to expert)

Lessons

One-hour lessons to learn and practice coding skills

Co-working hours

Work with experts on your research projects.

Community Building

Meet new people in your field! Learn from the best!

Events

Our upcoming and recent events

Our upcoming and recent events

Who We Are

We are a community of life science researchers from SILS and IBED institutes.

Board members

Tijs Bliek

Board member

Expertise & Interests:
  •  Genomics
  •  Snakemake
  •  RNA-Seq

Zsofia Koma

Board member

Expertise & Interests:
  •  Spatial analysis (GIS)
  •  Python
  •  Databases
  •  Machine Learning

Marc Galland

Community lead

Expertise & Interests:
  •  Genomics
  •  Snakemake
  •  Data Science

Like Fokkens

Board member

Expertise & Interests:
  •  Comparative genomics
  •  Python
  •  Phylogeny

Huub Hoefsloot

Board member

Expertise & Interests:
  •  Statistics
  •  Mathematical modelling
  •  Teaching

Joachim Goedhart

Board member

Expertise & Interests:
  •  Molecular Cytology
  •  Data Science
  •  R
  •  Shiny

Stacy Shinneman

Board member

Expertise & Interests:
  •  R
  •  Geospatial data

Johannes van De Groeve

Board member

Expertise & Interests:
  •  Databases
  •  SQL

Evelien Jongepier

Board member

Expertise & Interests:
  •  Microbiome
  •  Bioinformatics
  •  QIIME

Past and regular contributors

Jihed Chouaref

past contributor

Expertise & Interests:
  •  ChIP-Seq
  •  Snakemake
  •  Genomics

Pietro Marchesi

regular contributor

Expertise & Interests:
  •  Machine Learning
  •  Python

Joeri Jongbloets

past contributor

Expertise & Interests:
  •  Data visualisation
  •  R

Pim Schravendijk

past contributor

Expertise & Interests:
  •  Scientific programming
  •  Workflows

Caspar Treijtel

regular contributor

Expertise & Interests:
  •  Python
  •  Carpentry workshops

Mariette van Selm

regular contributor

Expertise & Interests:
  •  Research Data Management
  •  Figshare

Fred White

former board member

Expertise & Interests:
  •  Feature selection
  •  Data Science
  •  R

Max van Hooren

former board member

Expertise & Interests:
  •  RNA-Seq
  •  R

Susanne Wilken

former board member

Expertise & Interests:
  •  Marine Biology
  •  Microbial Ecology
  •  R

Emiel van Loon

former board member

Expertise & Interests:
  •  Statistics
  •  R
  •  Modelling

Franka van der Linden

former board member

Expertise & Interests:
  •  Molecular Cytology
  •  Data Science
  •  R

help

Click on 'Request assistance' to get help. Then select "New issue" and describe your request

Feel free to contact us

Stay in touch using the Slack workspace, mailing list or through emails




Presentations

Sarah Stolle - From PhD to Data Scientist DOI
A presentation by Sarah Stolle on her recent transition from PhD student to Data Scientist in industry (December 4, 2018)

Daphné van Beek - Data Stewardship Best Practices DOI
A presentation by Daphné van Beek, data steward at the Utrecht UMC on Data Stewardship and Data Management (April 7, 2018)

Marc Galland - Homo Biologicus Informaticus DOI
A presentation by Marc Galland on what the future life scientist should know regarding scientific programming, data analysis and management. (February 11, 2019)

Frans van der Kloet & Benjamin Thiombiano- Preprocessing DOI
A presentation on metabolomics data preprocessing (June 18, 2019)

Lessons

From messy to tidy using tidyverse and to ANOVA
A lesson on how to convert a "messy" dataset into a tidy one which allows you to perform filtering, plotting and ANOVA tests smoothly

Submit your NGS and metabolome datasets to public repositories for publication
This lesson covers the submission of Next-Generation Sequencing and GC-MS/LC-MS datasets to the NCBI Gene Expression Omnibus and EBI Metabolights public repositories.