Community Meeting Highlights and Updates

The Community Meeting on the 21st of March 2024 was filled with collaborative opportunities for developers, committers, and contributors working on federated analysis algorithms using Vantage6. The meeting covered infrastructure and algorithm development, recent releases, security patches, and features like the Researcher UI and Algorithm Store. Exciting announcements included the upcoming Vantage6 workshop and the roles defined within the Vantage6 community. Attendees were encouraged to share their work, align development efforts, and report bugs through the issue tracker. Overall, the meeting aimed to foster collaboration and streamline efforts within the community.

• Community Meeting
• Collaboration
• Vantage6
• Development
• Algorithms

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Presentation Transcript

1. Community meeting 21stof March 2024 This meeting will be recorded

2. The community Infrastructure Developers Committers & contributors Algorithm Developers Creating federated analysis algorithms Users Use vantage6 for privacy preserving analysis

3. Aim Collaboration opportunities Finding common interests by sharing what you are working on Align development efforts Avoid doing things twice Bug reports Please submit these in our issue tracker: https://github.com/vantage6/vantage6/issues

4. Agenda 11:00 Short introduction 11:05 Announcements and upcoming events 11:10 Recently released 11:25 Infrastructure development 11:40 Algorithm development 11:55 Miscellaneous

5. Announcements and upcoming events Vantage6 workshop Save the date: 9-10 October 2024 Organized by eScience center and IKNL. Spread the word! Vantage6 community roles defined! Contributors People that have opened pull requests which have been merged Members Members of the vantage6 Github organization Administrators Administrators of the vantage6 Github organization

6. Recently released 4.2.0-4.3.2 (7 releases)

7. Security patches An extensive penetration test has been executed on the vantage6 software in the context of one of the projects that IKNL and Maastricht University participate in. No high risks were identified; all risks that were found have now been mitigated, part in release 4.2.0 and others in 4.3.0 Contributors: Bart van Beusekom, Frank Martin (IKNL); Luis Sanchez Gomez (MDW)

8. Feature: Researcher UI The old User Interface was simple and more of a management tool around the API. The new UI has a more researcher-centered perspective that facilitates sending tasks and showing graphs based on algorithm metadata. Contributors: Richard Leurs, Elastique; Bart van Beusekom, IKNL; Frank Martin, IKNL

9. Feature: Algorithm Store It is difficult to get an overview of existing vantage6 algorithms, and except for the docker image not much information is available. The algorithm store will be a new service that manages algorithms for your project. The store will also establish trust in algorithms because it will be clear who is developer / reviewer / owner etc. Contributors: Bart van Beusekom, Frank Martin (IKNL); Djura Smits, Walter Baccinelli (eScience Centre) Estimate: Q1 2024 (early version with only a list of algorithms; full version later in 2024) [Feature Request] Algorithm store

10. Feature: New package vantage6- backend-common The code of the algorithm store is very similar in structure to the vantage6 central server. To prevent code duplication, this new package has been introduced. Note that we could have put all this code in vantage6-common, but that would have greatly increased the number of dependencies there (and therefore installation process for those users that only need to run the Python client) Contributors: Bart van Beusekom, IKNL; [Change] Remove algorithm store dependency on vantage6.server

11. Feature: Add Study concept Some collaborations consist of multiple studies. Sometimes, not all organizations take part in all studies. It would therefore be beneficial to create a Study , which is just a subset of organizations of a collaboration with a specific name. The idea is that tasks sent for this study then automatically select the right subset of nodes as well. Contributors: Bart van Beusekom, IKNL; Frank Martin, IKNL [Feature Request] Add study concept

12. Feature: v6 test A set of CLI commands to test the > v6 test --help Usage: v6 test [OPTIONS] COMMAND [ARGS]... vantage6 infrastructure Contributors: Bart van Beusekom, Execute tests on your vantage6 infrastructure. IKNL; Frank Martin, IKNL Options: --help Show this message and exit. Estimate: Q1 2024 Commands: feature-test Run diagnostic checks on an existing vantage6 network. integration-test Create dev network and run diagnostic checks on it. [Feature Request] Generic preprocessing before running algorithm

13. Feature: v6 dev extensions Give extra node or server configuration snippets to `v6 dev create-demo-network`, so that --extra-server-config PATH YAML File with additional server configuration. This will be appended to the server configuration file --extra-node-config PATH YAML File with additional node configuration. This will be appended to each of the node configuration files you can e.g. run a UI with it automatically or insert VPN configuration. Contributors: Bart van Beusekom, IKNL

14. Other changes 16 bugfixes 17 changes 10 features 10 security patches For more details on minor features and resolved bugs, see https://docs.vantage6.ai/en/main/release_notes.html

15. Infrastructure development Upcoming features and changes

16. Feature: Algorithm Store review process The current algorithm store is filled via a one-step process: an authorized developer can put the algorithms directly in the store. Plan is to have new roles: reviewers and store owners. Store owners assign a new algorithm to be reviewed. Only when this is complete, will the algorithms be available to users to be run. Contributors: Bart van Beusekom, Frank Martin (IKNL); Djura Smits, Walter Baccinelli (eScience Centre) Estimate: Q2-3 2024 [Feature Request] Algorithm store

17. Feature: visualizing algorithms in the UI The algorithms in the algorithm store are currently visible in a limited way in the UI: only the algorithm names are available from a dropdown when you start a task. The purpose here is to properly visualize algorithms in the UI. Also, more metadata on the algorithms should be included in the store, which should also be visualized. Contributors: Bart van Beusekom, Frank Martin (IKNL); Djura Smits, Walter Baccinelli (eScience Centre) Estimate: Q2-3 2024 [Feature Request] Algorithm store

18. Feature: External authentication Currently the users access though vantage6 credentials (username and password), but we want to allow them to use external identity providers such as Microsoft, Google, GitHub, etc. to authenticate. Contributors: Walter Baccinelli (eScience Center), Djura Smits (eScience Center) Estimate: Q2 2024 [Feature Request] Login using external identity provider #917 vantage6/vantage6 (github.com)

19. Feature: Algorithm container chaining Split responsibilities of the algorithm containers: Data extraction Preprocessing Algorithm (federated / central) It has the following advantages: The different components can be used modular. The UI/UX task flow more consistent for different data source types. Reuse the data-extraction / pre-processing step for multiple analysis making it quicker and less error prone Contributors: Frank Martin (IKNL), Bart van Beusekom (IKNL), Estimate: Q2-3 2024 [Feature Request] Chaining of algorithm containers Issue #943 vantage6/vantage6 GitHub

20. Feature: support for algorithms on alternative containerization technologies. Decoupling v6-Node and specific containerization technologies (Docker) through abstractions. Motivation: (1) podman used by default on RHEL and some hospitals infrastructure. (2) open/closed principle in this aspect, with Docker and Podman as the first two supported technologies. Contributors: H ctor Cadavid (NLeSC) Estimate: Q1-2024 https://github.com/bdh- generalization/requirements/issues/7

21. Feature: template tasks Currently, a task has to be defined in its entirety every time you create a new task. This is not very convenient if you are often repeating the same types of analyses. The idea is to create a template task where a number of the settings are fixed, so that you can easily create a new task from the template Contributors: Bart van Beusekom, IKNL Estimate: Q2-3 2024 [Feature Request] Template tasks

22. [Feature] Algorithm preprocessing For example: Data transformation Feature Engineering Stratification Discretization Filtering Contributors: Harm Buisman, Bart van Beusekom , Frank Martin (IKNL) Estimate: Delayed waiting for algorithm chaining [Feature Request] Generic preprocessing before running algorithm

23. Algorithm development

24. Euracan Algorithms Algorithm suite for the Euracan (European cancer registry) project. These are made for v2.3.4 and will be ported to version 4 later this year. Summary Cross tabulation Chi-squared CoxPH (+assumption test) Kaplan-Meier Log Rank Test GLM IKNL/v6-euracan-algorithms: Vantage6 algorithms for the EURACAN project (github.com)

25. Miscellaneous

26. Miscellaneous Questions Finding common interests by sharing what you are working on Feedback Finding common interests by sharing what you are working on Ideas Finding common interests by sharing what you are working on