The UvA is fully committed to the principles of Open Science, emphasizing transparency and reproducibility in research. Open Science involves making scientific research freely accessible to everyone in society, ensuring research results are widely available. Open Science follows the FAIR (findable, accessible, interoperable, reusable) principles. To ensure Open Science, for every project, whether it is a grant, a publication or a student project, the following general four guiding rules hold.
It is crucial to:
To further support good data management practices, IBED provides a Data Management Bonus of 1000 euro to PhDs and Postdocs who succeed, by the end of their project, to deliver such a well-organized and self-contained archive. To support research at scale, this page describes computational resources available for IBED. The document provides both guidelines and resources (Storage, Archiving, HPC). We conclude with a list of resources for courses and trainings offered by UvA, including good data management and computational practices. This document is tailored to IBED, but for more generic information on available resources at faculty level check Data Analytics and Statistics Hub (DASH).
For almost all funding agencies a Data Management Plan (DMP) is a requirement. To prepare your DMP it is recommended to create an account at DMPonline. Most likely the template of your grant (e.g. NWO) will be available within the platform. Alternatively, you can use a template of the funding organization. Prepare your DMP and invite the IBED data steward (Johannes De Groeve) for review to check if the DMP is in line with FNWI RDM policy and institutional RDM protocol. For examples of successful DMPs within IBED, please check here.
Typical questions and topics which are addressed in a DMP include:
Answering these questions will streamline decisions about which computational resources you require during the project, including which type(s) of institutional storage are most applicable and which High Performance Computational needs there are. Moreover, it will help you to define better a well defined project directory structure. DMP’s are often only created when obliged by funders. However, whether you are a student or a PI, it is always recommended to think in advance about the above questions.
This will help with:
A common issue that most students and PI’s encounter is how to keep their project organized. The starting point to keep your project organized is to define a project directory structure for each individual project unit (e.g. a manuscript, Bsc/Msc thesis). The directory structure and what can be defined as a project unit, is based on knowledge that you gained from your project proposal’s roadmap and DMP. While project units can change over time it is good to have an initial starting point of basic organisation. Here we provide some basic examples. To set-up basic R-project please check the following tutorial [TO BE CREATED].
Basic project directory structure
Example 1
.
├── README.md
├── code
│ ├── 0_data_preparation.Rmd
│ └── 1_analysis.Rmd
├── data
│ ├── input
│ └── output
├── docs
│ ├── manuscript.docx
│ ├── figs
│ └── tabs
└── project_name.RprojExample 2
.
├── README.md
├── code
│ ├── 0_data_preparation.Rmd
│ └── 1_analysis.Rmd
├── data
│ ├── raw
│ └── processed
├── docs
│ ├── manuscript.docx
│ ├── figs
│ └── tabs
└── project_name.RprojTo be in line with institutional policy, prior to publication, researchers need to ensure research data is accessible through an institutional cloud storage solution. Depending from the needs including size, speed, resources, programmatically accessibility, etc. different storage solutions are offered to IBED staff and students. Here we list all the storage resources which can be used for ongoing research.
At closure of a project (student, publication) data and code are required to be published in a data repository following the Open Science and FAIR principles. Many general purpose and domain-specific repositories exist (see below).
An important general purpose repository is Figshare, for which UvA provides an UvA/AUAS institutional account for every staff member. Note that BSc and MSc students do not have access to the institutional Figshare. BSc and MSc students can create accounts and upload files up to 5GB for open data and materials. However, we highly recommend researchers to invite students by creating a “project” via their institutional account. Through this venue the research data is accessible to the PI in a public repository owned by UvA and there are no storage limitations.
There are several options available to IBED staff and students who need extra computing capacity. We distinguish two Virtual Research Environments (VRE, Research Cloud) and three clusters (Crunchomics, Snellius, Spider / Grid). See the full list below.
Before applying for HPC resources, consider the following questions:
The Computational Support Team can help people decide which option to use. The student or staff member should then contact the service’s help desks to get access and troubleshoot specific problems.
Imagine you have a piece of code, and you’re keen on tracking its changes without losing the original version. The conventional method involves saving scripts as new files, often labeled with indicators like ‘v0’ or a timestamp. Git offers a more seamless way to version your code without the hassle of managing different version files manually. It not only tracks changes made to your files but also equips you with tools to document those changes. While Git’s initial development focused on code versioning, it’s versatile enough to handle versioning of smaller datasets. GitHub and GitLab support various text file formats (e.g., csv, fasta), making them ideal for versioning.
Please submit an issue for improvements to the documentation, or contact the Computational Support Team of IBED.