events organised 2017 - 2022
- Statistics for biologists – 21 June 2022 – 14.00 to 16.00.
Two hours dedicated to basic statistics for biologists. After this event, you will be able to better understand how to decide on the number of biological replicates needed for your experiment, get basic notions on inference statistics and apply it to your daily work. People involved: Marc Galland, Emiel van Loon.
- 16S, ITS etc amplicon sequencing – June 2, 2022 – online. A morning with the basics and not-so-basics of metabarcoding. The first half is general (aims and requirements of the research questions tackled by metabarcoding & overview of method; from sample to sequencing data; aims, approaches, and options of data processing steps & annotation; persistent problems), the second focuses on a DADA2-based workflow (dadasnake workflow for amplicon processing; spoiled for choice: more details on target- and technology-specific options for data processing & annotation, e.g. ITS for fungi, by-catch-heavy targets like AMF or archaea; different Illumina-sequencers/protocols). Organized by Anna Heintz-Buschart.
- Introduction to the Crunchomics compute cluster – May 10, 2022 – Science Park 904.
An afternoon dedicated to the SILS/IBED Crunchomics computing cluster. After a small introduction to the Crunchomics system, a demonstration of how to connect to crunchomics and how to execute a genomic pipeline will be given.
We will guide you regarding connection using the ssh protocol, navigating the file system using Shell commands and how to create an environment dedicated to your needs using conda. We will then dig deeper by introducing the SLURM queuing system for batch jobs.
People involved: Marc Galland, Evelien Jongepier, Wim de Leeuw, Han Rauwerda.
!! Important !! Please follow the instructions here to make sure that you have a working installation of the Unix Shell.
To register: https://www.eventbrite.co.uk/e/252944743537
- Data Carpentry workshop “Data Analysis and Visualization in Python for Ecologists” – April 21 and 22, 2022 – Science Park 904 and Roeterseiland Campus.
Python is a general purpose programming language that is useful for writing scripts to work effectively and reproducibly with data. This is an introduction to Python designed for participants with no programming experience. This workshop was taught over two days. It started with some basic information about Python syntax, the Jupyter notebook interface, and move through how to import CSV files, using the pandas package to work with data frames, how to calculate summary information from a data frame, and a brief introduction to plotting. The last lesson demonstrated how to work with databases directly from Python. This workshop is organised by Tijs Bliek and Marc Galland (members of the Amsterdam Science Park Study Group), Iris van der Knaap (Data Science Center, University of Amsterdam) and Sam Nooij (Leiden University Medical Center).
- Metagenomics 101, first session 16 February 2022 at 1:30 pm in Science Park B1.25, organized by Anna Heintz-Buschart. Details to be announced, or contact Anna directly.
- Data Carpentry with Python – Dec 6 to 9, 2021 – online.
This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing. This workshop is designed to be taught over two full days of instruction. Members from the Amsterdam Science Park Study Group are involved in the organization and as helpers during the workshop. This event is organised by the eScience Center in the mornings of December 6 to December 9, 2021.
Workshop lesson materials: https://esciencecenter-digital-skills.github.io/2021-12-06-dc-socsci-python-nlesc/
- Data skills for genomics workshop, 30 November & 1 December 2021, online
This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing. This workshop is designed to be taught over two full days of instruction. Members from the Amsterdam Science Park Study Group are involved in the organization and as helpers during the workshop.
- Git, Shell and R: an introduction to programming, 9 & 11 November 2021, onlineA two-day workshop to promote good practices in scientific programming. This workshop gives an introduction to the Shell command-line, version control with git and data analysis with R. This course is organized by the UvA Library in collaboration with the Carpentries Foundation.
- First Study Group Summer School – Online – June 21 to July 2, 2021.
The first edition of the Amsterdam Science Park Study Group Summer School consisted of a series of two-day workshops designed to teach basics as well as more advanced topics in scientific programming. This Summer School gathered beginners and more advanced participants alike to enhance the quality and efficiency of their research. Learning basic and domain-specific programming skills is meant to improve the quality of research findings but also promote a more Open Science.
- Data Carpentry Genomics workshop, Science Park 904 – G2.02, 30 August 2020, 09:00:00 AM
The focus of this workshop is on working with genomics data, data management and analysis for genomics research, including best practices for organization of bioinformatics projects and data, use of command line utilities, use of command line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing.
- Good practices in programming, Science Park 904, B1.25, 14 May 2020, 02:00:00 PM
This event is a private event for board members of the Study Group.
- Data Carpentry Geospatial Data workshop, Science Park 904, different rooms (to be annonced), 12 March 2020, 09:00:00 AM
This workshop is developed with the National Ecological Observatory Network (NEON). It focuses on working with geospatial data – managing and understanding spatial data formats, understanding coordinate reference systems, and working with raster and vector data in R for analysis and visualization. Workshop dates are now definitive.
- Docker and Singularity workshop, Science Park 904, B0.208, 4 March 2020, 01:00:00 PM
This event is a private event for board members of the Study Group.
- Computational skills for life sciences., Science Park 904, different rooms (see workshop website), 3 December 2019, 09:00:00 AM
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills.
- Introduction to Open Data Science with R., Science Park 904, different rooms (see workshop website), 20 November 2019, 09:30:00 AM
This lesson will introduce you to open data science so you can work with data in an open, reproducible, and collaborative way. Open data science means that methods, data, and code are available so that others can access, reuse, and build from it without much fuss. Here you will learn a workflow with R, RStudio, Git, and GitHub.
- Analyzing metabolomics data with R – Benjamin Thiombano & Frans van der Kloet, Science Park 904, room D1.115, 18 June 2019, 04:00:00 PM
In this session, we will cover analysis of raw exported GCMS data (.mzxml) using R
- Using Docker to improve software reproducibility – Zsofia Koma & Like Fokkens, Science Park 904, room D1.113, 4 June 2019, 04:00:00 PM
Containerization using Docker and Singularity can help to improve research code reproducibility. Discover how during this event!
- Build genomics pipelines using Snakemake – Tijs Bliek & Marc Galland, Science Park 904, room D1.110, 21 May 2019, 04:00:00 PM
Discover how to build workflows for genomics using the popular Snakemake tool.
- Make your first online R Shiny online application – Joachim Goedhart, Science Park 904, room G5.29, 14 May 2019, 04:00:00 PM
See how you can create a Shiny online application that runs R code without the need for users to code! In this interactive session, Joachim Goedhart (Assistant-Professor@Molecular Cytology) will explain you how.
- Visualization of RNASeq results – Susanne Wilkens & Fred White, Science Park 904, room A1.06, 7 May 2019, 04:00:00 PM
How to make heatmaps, clustering analysis and much more from RNA-Seq results.
- Introduction to the Julia language – Like Fokkens & Emiel van Loon, Science Park 904, room D1.112, 23 April 2019, 04:00:00 PM
Discover the Julia language for scientific programming
- ImageJ hands-on session – Franka van der Linden, Science Park 904, room B0.207, 9 April 2019, 04:00:00 PM
A practical introduction to ImageJ
- Discovering HUGO to create websites – Zsofia Koma & Tijs Bliek, Science Park 904, room D1.110, 26 March 2019, 04:00:00 PM
What is the website generator HUGO and how you can use it to generate custom academic pages to enhance your visibility and career prospects.
- Brainstorm session on organising lab notebooks and data in an understandable way – Franka van der Linden & Marc Galland, Science Park 904, room A1.10, 12 March 2019, 04:00:00 PM
This is a brainstorming session to know what your collegues think of your experimental documentation and think about ways to improve it. We will also see how to improve online data retrieval.
- RNA-Seq hands-on workshop – Max van Hooren, Tijs Bliek, Marc Galland and Ernest Aliche, Science Park 904, room G3.10, 7 March 2019, 01:00:00 PM
Come and discover the power of RNA-Seq during a practical afternoon session
- Data about the data – Marc Galland & Like Fokkens, Science Park 904, room A1.10, 26 February 2019, 04:00:00 PM
Learn the requirements for submitting data to public repositories (e.g. NCBI SRA)
- Exploring the R tidyverse package and performing statistical tests – Marc Galland, Science Park 904, room A1.10, 19 February 2019, 04:00:00 PM
The tidyverse package for R has become one of the standard package to use for data manipulation and visualisation. See why in this episode! We will also perform some ANOVA and post-hoc tests.
- Data Carpentry Genomics workshop – Mattias de Hollander, Like Fokkens & Marc Galland, Wageningen University (room tba), 5 February 2019, 09:00:00 AM
A two days Carpentry workshop to discover tools and good practices related to genomic analyses
- Principal Component Analysis (PCA) – Huub Hoefsloot & Marc Galland, Science Park 904, room A1.14, 29 January 2019, 04:00:00 PM
Principal Component Analysis is a tool to bring out patterns in your (big) data. It can be used to visualize and explore data. In this hand on tutorial PCA will be explained in simple terms. Further it will be shown how to do a PCA and how to visualize the results in R. After this one-hour session you should be able to do a PCA on your own data. If you bring your data (not too big, please) we could even try to do some work within this hour.
- Software Carpentry workshop on Python programming, Amsterdam, Roeterseiland Campus, 14 January 2019, 09:00:00 AM
This two days 100% hands-on workshop will teach you major concepts in programming using Python to exemplify it.
- Tidy up your data – Emiel van Loon, D1.110, 11 December 2018, 04:00:00 PM
Learn how to create and work with a clean ‘tidy’ dataset.
- From PhD student to Data Scientist/Software Engineer – Sarah Stolle & Till Bey, D1.112, 4 December 2018, 04:00:00 PM
Discover how more expertise in programmming & data analysis can enhance your science and broaden your career perspectives
- Basic statistics – Emiel van Loon, D1.114, 20 November 2018, 04:00:00 P
Survival statistics for the modern Life Scientist
- Enhanced data visualization in R using ggplot and plotly – Marc Galland & Marijn Knip, C4.174, 6 November 2018, 04:00:00 PM
How can you visualise a complex dataset using R advanced graphical libraries? See a demo and get some hands-on experience!
- RNA-Seq data visualisation – Max van Hooren, D1.115, 30 October 2018, 04:00:00 PM
Learn how to make complicated figures to visualise RNA-seq data.
- Study Group Opening Session, SILS common room, 16 October 2018, 04:00:00 PM
Join this event to know more about the Study Group and learn how to improve programming skills and speed-up your data analysis
- Hacky Hour !!!, Oerknal Café, 3 July 2018, 05:00:00 PM
- Metabarcoding for Microbial Ecology by Susanne & Marc, B0.203, 26 June 2018, 05:00:00 PM
To study the microbiome of a given environment (gut, soil), 16S rRNA amplicon sequencing has proven to be a very powerful technology to profile the microbial community. Come and join for a one-hour hands-on practical session.
- Hacky Hour !!!, Oerknal Café, 19 June 2018, 05:00:00 PM
- Spatial data visualisation by Zsofia, B0.203, 12 June 2018, 05:00:00 PM
Spatial data visualisation (Python)
- Hacky Hour !!!, Oerknal Café, 5 June 2018, 05:00:00 PM
- Machine Learning applications in Biology by Zsofia/Stefania/Marc, room B0.203 (Science Park 904), 29 May 2018, 05:00:00 PM
Machine Learning applications are gaining momentum in biology. Come and see how one Machine Learning method (Random Forest) can be applied to your research to gain more insights and prediction power.
- Hacky Hour !!!, Oerknal Café, 22 May 2018, 05:00:00 PM
- Research Data Management by Christine Staiger & Caspar Treijtel, room B0.203 (Science Park 904)”, 15 May 2018, 05:00:00 PM
A lesson on Research Data Management (abbreviated RDM). First, Christine will make a short intro on RDM and where SURFsara solutions can help. Then, Caspar will demo the FigShare solution on an example dataset.
- Hacky Hour !!!, Oerknal Café, 8 May 2018, 05:00:00 PM
This Hacky Hour will follow-up on the Experimental Design lesson from last week. Also some help on Unix loops and genomic pipelines.
- Understanding experimental design by Marc and Emiel, B0.203, 1 May 2018, 05:00:00 PM
What is experimental design? How can you better plan your experiments?
- Hacky Hour !!!, Oerknal Café, 24 April 2018, 04:00:00 PM
Workflow & gene counts matrix comparison
- The PI data workshop Data Stewardship, Research Data Management by Marc, B0.203, 17 April 2018, 05:00:00 PM
Research Data Management at Utrecht UMC & the SILS/IBED data clinic proposal
- Hacky Hour !!!, Oerknal Café, 10 April 2018, 05:00:00 PM
- Comparative Genomics using Circos by Like, B0.203, 3 April 2018, 05:00:00 PM
Use the Circos program to compare genomes
- Make your own personal website using GitHub by Carlos, B0.203, 20 March 2018, 05:00:00 PM
Use the online Github platform to make your own (academic) website (CV, publications, talks, etc.)
- Regression analysis by Emiel, B0.203, 6 March 2018, 05:00:00 PM
Simple and multiple linear regressions in R.
- Hacky Hour on RNA-Seq analysis, Café Oerknal, Science Park (next to the USC Sport building), 27 February 2018, 05:00:00 PM
A co-working session at Oerknal to continue the lesson on RNA-Seq analysis.
- RNA-Seq analysis by Max van Hooren and Fred White, B0.203, 20 February 2018, 05:00:00 PM
A one-hour lesson on how to perform RNA-Seq analysis.
- Exploratory data analysis with R by Joeri and Marc, B0.203, 6 February 2018, 05:00:00 PM
In this lesson we will explore a few useful functions to get basic statistics on the dataset and make exploratory plots.
- Handling databases with Python by Zsofia, B0.203, 23 January 2018, 05:00:00 PM
Managing research info in databases is a crucial skill for any researcher now. Here, it will be shown how to do it with Python and R.
- Common Workflow Language with Pim, Room B0.203, 9 January 2018, 05:00:00 PM
The CWL specification helps to describe workflows in a way that makes them portable and scalable across a variety of software and hardware environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry.
- Workshop Pipelines in Python, D1.113, 19 December 2017, 05:00:00 PM
In this 1 hour workshop we will discuss how pipeline design can assist in project and data management. We will demonstrate a few Python libraries that are frequently used in this context.
- Sinterklaas Data Hacky Hour, Oerknal Café, Science Park campus, 5 December 2017, 04:00:00 PM
Sinterklaas is among us. As his little helpers, we’ll help you to analyse your data in one dedicated session.
- Hacky Hour on statistics, Oerknal Café, Science Park 904, UvA, 28 November 2017, 05:00:00 PM
Discover the power of statistics on your own data using R. This will be a BYOD (Bring Your Own Data) workshop!
- “Statistical tests with R” by Emiel van Loon, Room D1.113, Science Park 904, UvA, 21 November 2017, 05:00:00 PM
Discover the power of statistics on your own data using R. This will be a SYOD (Send Your Own Data) workshop!
- “Simple plots with R” by Joeri Jongbloets, Room D1.113, Science Park 904, UvA, 7 November 2017, 05:00:00 PM
Make simple graphs and plots on your data using R
- “Explore your data” by Pietro Marchesi, Room B0.206, Science Park 904, UvA, 24 October 2017, 05:00:00 PM
Describe your data and perform some data cleanup and plots using Python
- “One-hour introduction” to Python by Like Fokkens, Room B0.206, Science Park 904, UvA, 10 October 2017, 05:00:00 PM
This practical workshop will help you through the Python maze
- Second meeting for 2017/2018 academic year, Oerknal, 26 September 2017, 05:00:00 PM
Co-working event & initial plan for activities based on the first google survey
- First meeting for 2017/2018 academic year, Oerknal, 12 September 2017, 05:00:00 PM
We present an initial plan for activities in the new year, make new plans, and show some great self-tuition material.
- Closing summer session / Make a wish!, Science Park Oerknal, 25 July 2017, 04:00:00 PM
During this session, we will go through your learning and working wishes for the next academic year
- RNA-Seq / Co-working session, Science Park Oerknal, 11 July 2017, 04:00:00 PM
We will finish RNA-Seq analysis tutorial with Kallisto and Sleuth. Also co-working. Don’t forget to bring your own laptop!
- Collaborate with your colleagues using Git and GitHub., Science Park 904. Room C4.215, 13 June 2017, 04:00:00 PM
This session will be taught by Mateusz to show the power of collaboration for code building. Don’t forget to bring your own laptop!
- Building pipelines with Snakemake / Co-working session., Science Park Oerknal, 30 May 2017, 04:00:00 PM
Let’s meet again in Oerknal to learn code and solve practical issues. Don’t forget to bring your own laptop!
- Building pipelines with Snakemake / Co-working session., Science Park Oerknal, 16 May 2017, 04:00:00 PM
Let’s meet again in Oerknal to learn code and solve practical issues. Don’t forget to bring your own laptop!
- Second meeting., Science Park Oerknal, 2 May 2017, 04:00:00 PM
Lets meet again in Oerknal for some code learning. Don’t forget to bring your own laptop!
- Fist Study Group Meeting Ever in Science Park, Science Park Oerknal, 18 April 2017, 05:00:00 PM
Short introduction to Study Groups. First co-working session together!