WHO WE ARE
Board members are involved in the organization of data and code-related events, the promotion of Open Science values (open data, open code, good practices in programming, etc.). Board members belong to various institutes and departments of the University of Amsterdam:
- The Swammerdam Insititute for Life Sciences (SILS,)
- The Institute for Biodiversity and Ecosystem Dynamics (IBED),
- The Data Science Center (DSC), part of the University Library.
Board members are listed below in alphabetical order.
Lab technician in the department of Plant Development and (Epi)Genetics (SILS, UvA). My training and work experience focused on molecular biology techniques and as such I currently run the department “wet lab”.
About 3.5 years ago I joined the first “hacky hours” and took my first steps in bioinformatics out of the lab’s need for up-to-date data analyses. The purpose of these hours was to help people struggling with bioinformatics and since then I developed “drylab” skills and was able to support my team in a different way.
Expertise: Genomics, bioinformatics, Snakemake, R
Main community role: Trainer (genomics, R)
Co-founder and current community lead of the Amsterdam Science Park Study Group. Originally trained as a “wet-lab” Plant Molecular Biologist, I progressively drifted towards Genomics, Data Management and Data Science with R and Python. Presently, I work as a support scientist for students and colleagues involved in genomics and other “omics” intensive research taking place in the Green Life Sciences research cluster.
Since 2020, I am part of the Data Science Center of the University of Amsterdam as a Data Scientist and as part of the Coordination Team.
Expertise: R, Python, genomics, git/GitHub, Machine Learning.
Main community role: Community Lead, Webmaster, Grant applications.
Links: UvA webpage, personal website, LinkedIn, ORCID.
I used to be a fully-fledged wet-lab molecular microbiologist, but I got fed up with my error bars always being bigger than everyone else’s. So, after my PhD in 2011, I fell back on my inclination towards programming, data visualization, critical thinking, and autodidacticism, and built myself a career in bioinformatics of microbiomes.
I joined SILS and the Amsterdam Science Park Study Group in 2021 as Assistant Professor in Microbial Metagenomics. I love interacting with both data-dazzled wet-lab people, data science nerds, and my esteemed colleagues who understand maths way better than I do. I strongly believe in community-driven bottom-up Open Science research and making the most of hard-earned biological data.
Expertise: Meta-omics, multi-omics integration, bioinformatics, numerical ecology, workflow management, R, python, perl, bash, NoSQL databases, bioinformatics data repositories.
Links: UvA webpage, GitHub homepage, Twitter, Google Scholar.
Iris van der Knaap
Coordinator Digital Skills at the library of the UvA/HvA and member of the the coordination team of the UvA Data Science Center. In my role at the library, I am expanding and further developing our training and support in digital skills for researchers of the UvA.
I have joined the Amsterdam Science Park Study Group in 2021 to learn from their experience in community building and organizing trainings, to create a direct link to centralized support and to stimulate collaboration in data science throughout the UvA. I have a Research Master in the History of Science from Utrecht University and have worked for about five years at Utrecht University Library as the subject librarian history 1500-present. In this role I provided support on Open Science, RDM, copyright, information literacy, with a specific focus on Digital Humanities and online research visibility.
Expertise: Open Science, research visibility.
Main Community roles: training coordination, community building, centralized support.
Links: UvA profile, LinkedIn , ORCID
As a Geoinformatician for the Institute for Biodiversity and Ecosystem Dynamics computational support team, I support scientific staff and students with geospatial data processing, management and visualization. I use my expertise in R, ArcGIS, SQL, Google Earth Engine or any other computational tool that best solves the problem. I enjoy working on interdisciplinary, collaborative projects with multiple partners from across academia, industry, government and consulting. My work also includes fostering a collaborative work environment for researchers and students by ensuring that knowledge and skills are being communicated and shared efficiently which is why I joined the Amsterdam Science Park Study Group in 2019.
Expertise: R, Geospatial data analysis, GIS, community management.
Main community roles: Training Coordinator, Trainer (geospatial data).
Links: UvA webpage, LinkedIn.
Regular contributors are experts that participate regularly to the Amsterdam Science Park Study Group activities upon request from board members. Their complementary expertise and involvement in research and teaching are immensely useful during training workshops, data consultancy hours or co-working sessions.
Regular contributors are listed below in alphabetical order.
JOHANNES DE GROEVE
I currently work as an Associate Professor in the Biosystems Dana Analysis department (SILS), and I am also program director of the MSc Systems Biology and Bioinformatics. The aim of our research is to develop and validate methods for organising, summarising and visualising complex biological data for systems biology through the integration of bioinformatics and biostatistics. Our department is an important hub within the SILS institute in providing support for advanced Data Analysis. The amount of “big data” is growing exponentially due to technical developments. It is not uncommon to measure metabolomics, proteomics, gene-expression and, also recently, microbiome and RNA-seq data on the same biological system, e.g., in plants. This creates challenges for the data analysis, since these data needs to be analysed simultaneously to arrive at a sensible interpretation of the underlying biological processes. Moreover, such data needs to be combined with available background knowledge. There is a growing need for support in the analysis of such data sets, which asks for high-level trained staff since this type of data analysis is very advanced, and even has to be developed to a certain extent. The Amsterdam Science Park Study Group is an excellent platform where we can find each other to improve each other data skills.
Expertise: biological networks, statistics, modelling.
Main community role: data consultancy on statistics and experimental design.
Links: lab web page.
My background is in evolutionary biology, specifically of insects. Since 2019 I am a dedicated bioinformatician in the IBED computational support team. I develop teaching material for practicals and assignments. In addition, I offer on-demand workshops in bioinformatic methods for students and scientists and support their access to the computational infrastructure. To ensure we are ready for increasing demand for FAIR research data storage, I am involved in the iRODS pilot of SURF Sara. As a board member of the Amsterdam Science Study group I am happy to contribute to Data and Software Carpentry courses and I welcome ideas and topics for workshops.
Expertise: bioinformatics, microbiome (QIIME), R, Linux.
Main community roles: trainer (microbiome)
I have worked as bioinformatician and biostatistician with omics data in various different research projects ranging from ecogenomics, toxicogenomics and (biomedical/clinical) biomarker studies.
I work in the RNA Biology and Applied Bioinformatics group (RBAB), and the Molecular Analysis Department (MAD) at the Swammerdam Institute for Life Sciences, University of Amsterdam. The RBAB group is mainly interested in the role of small RNA’s in biological systems. The MAD is a technology group that develops and applies molecular genomics technologies. I do have a broad interest and during my career I have provided bioinformatics expertise to many research projects in collaboration with many different scientists. The Amsterdam Science Park Study Group provides an excellent platform to share and to learn, and to meet other scientists.
Expertise: Transcriptome and genome data analyses, or in other words: the bioinformatics needed for analyzing different types of RNA and DNA sequencing data.
FRANS VAN DER KLOET
I have a training background in Analytical and Computational chemistry and did a PhD in quantitative aspects in/of high resolution mass spectrometry data in metabolomics, a post-doc on aspects of multi-block/view solutions like JIVE, DISCO and OnPLS and incorporating these types of methods in the prediction/classification of in vivo transcriptome data.
Another postdoc followed at the Amsterdam Medical Center where I was concerned with (pre)processing, analysing and combining multi-omics datasets. As of January 2019, I started as research assistant bioinformatics in the Biosystems Data Analysis group at SILS. As such I support bioinformatics and systems biology research in the RPA Systems Biology and in SILS. In this role it seemed only logical I would join the Study Group and they were quick to draft me for this great initiative where I learn and support in (pre) processing of large datasets and development of analysis tools including Machine Learning.
Expertise: multivariate data analysis, metabolomics, data fusion, Python, tool deployment (Galaxy, iRODS).
Main community roles: Research Data Management project (iRODS), helper at workshops.
Links: lab webpage, LinkedIn.
WIM de LEEUW
Main community roles: SILS and IBED compute cluster (Crunchomics) management.
I am a bioinformatician in the RNA Biology and Applied Bioinformatics group (RBAB), and the Molecular Analysis Department (MAD) at the Swammerdam Institute for Life Sciences, University of Amsterdam.
My focus lies on transcriptome dynamics, and I am interested in the role of small RNAs in biological systems. In the RBAB group, I am involved with the compute cluster for genomics called ‘Crunchomics’ and with the tape-archive facility of SILS.
Expertise: Transcriptome analyses, Crunchomics., Research Data Management.
FORMER COmmunity members
These amazing people helped the Amsterdam Science Park Study Group community for its activities. We are grateful for the help and inspiration they gave to the community👏👏🤝
- Jihed Chouaref, 2017-2019. Regular contributor involved in helping at Carpentry workshops and developing genomic pipelines using Snakemake. Currently postdoctoral researcher in human genomics at LUMC. LinkedIn profile.
- Like Fokkens, 2018-2021, board member. Active in Software Carpentry workshops and support on genomics and data visualisation. Currently a postdoctoral researcher at the UvA. UvA webpage.
- Max van Hooren, 2018-2020, regular contributor. instructor at RNA-seq dedicated events.
- Joeri Jongbloets, 2017-2019. Regular contributor. Instructor at R-dedicated events.
- Pietro Marchesi, 2017-2019. Regular contributor. Python trainer at workshops.
- Susanne Wilken, 2017-2019. Regular contributor. Trainer on microbiome amplicon sequencing.
- Franka van der Linden, 2018-2020. Board member. Active in organization of training events (image analysis).