Commit 8f23defe authored by Tensi, Annika's avatar Tensi, Annika
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Merge branch 'sub-sites' into 'main'

new events, gallery function, lighthouse

See merge request !22
parents d7868bbf af00ba92
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......@@ -7,6 +7,8 @@ url: /about/whoarewe/
---
![Picture of the OSC-W core group](/profilepicsmembers/2205coregroup.jpg)
Currently, we are a group of researchers and staff from WUR. Our community comprises academics and support staff from different disciplines and career stages. All researchers, students and support staff of WUR and NIOO-KNAW and at all career stages, are welcome!
Get to know us and find out why we are enthusiastic about Open Science.
......
---
title: 'Winner of the Lighthouse Award 2022'
author: "Annika Tensi"
output: html_document
date: '2022-06-03'
---
# Justin van der Hooft
![Picture of Justin giving his presentation at launch event](/images/Justin_launch_award.jpg)
## FAIRifying Multi-Omics Resources: the Paired Omics Data Platform
### Open Science Objectives & Practices
The Paired Omics Data Platform (PoDP) provides an effective solution to connect genomic, metabolomic, (and proteomic) data derived from a single biological source. It uses and promotes Findable, Accessible, Interoperable, and Reusable (FAIR) principles by requiring all datasets that are linked to be publicly available and accompanied by metadata. Furthermore, the PoDP adds a layer of metadata for the recorded links where existing field-specific ontologies are used where possible. Finally, the PoDP has a manual curation step and project version control.
### Introduction
Data-driven discovery of novel chemistry from natural sources can be greatly accelerated by applying multiomics approaches. Advances in (meta)genomic sequencing and increased sensitivity in metabolomic data acquisition are paving the way to our deepest understanding yet of the chemical language of microbial life. The synergy of multi-omics data analysis relies on access to well-documented, curated datasets from individual biological sources. While, nowadays, data sharing through public repositories for genomic or metabolomic data is becoming common, the connections between these types of data are hard and sometimes impossible to find. Yet, connecting genomes to metabolomics data enables multi-omics tools to facilitate structural elucidation of metabolic products, and to obtain additional information, such as mode of action, resistance mechanisms, and new enzymatic functions, that are not available from single omics approaches. Here, a platform was built that records annotated links between omics data types in human and computer-readable manner. The platform itself is available through docker and back-ups of the projects it contains can be found on Zenodo. Furthermore, version control is done for all the projects: if data is added or changed, this is logged and can be made visible to the user.
### Motivation
Multi-omics approaches are on the rise and the PoDP facilitates their development by recording paired data as well as validated links between genomes and mass-spectral data. This will assist in validating novel algorithms that - in turn - will spark the creation of novel paired data sets. The PoDP enables and encourages FAIR data exchange within the scientific community, an initiative that is widely accepted, but in practice more difficult to realise without an incentive. The PoDP gives incentive to researchers to make their data public, as this curated source for paired data sets makes it much more likely that their data will be reused and cited. The PoDP also has the potential to catalyse new collaborations between groups across the world to creatively re-analyse datasets and discover new biochemistry that would otherwise have remained buried in the data. Finally, by collecting both recorded omics data links as well as validated genomicmetabolomic entities therein, the platform also contributes to the development of novel algorithms, which is of benefit to tool developers like myself.
### Lessons learned
The funding of this research was part of a larger eScience grant. In general, to find funding purely for FAIRicifation of workflows or data is very difficult, and it is not always part of common practice (yet). We were able to present the platform at several conferences and seminars, and we will also integrate its use and existence in future workshops.
During the project itself, it was hard to to derive a minimal metadata list that was mutually agreed on as each laboratory (more than 100 researchers from >10 different countries were involved) has its own specific ways of doing things, and not everything is easily captured into (existing) ontologies. Furthermore, the (perceived) additional time to register paired omics data projects into the PoDP was also a factor of importance. Yet, the platform now contains an easy-to-fill form that accommodates most typical workflows. Michelle also bridged biochemistry and bioinformatics by designing a new community standard for paired data sets.
It is encouraging to observe that the platform is already picked up by the community and 75 novel entries have been made since the launch. Furthermore, the first tools that automatically connect gene clusters to mass spectra are integrating the platform and/or using the recorded paired data for training and validation.
### How much extra time did the open practices require?
Building the platform took quite some time, and maintaining it will also continue to take some time, as the construction is such that contributors can submit projects, which also makes it (more) vulnerable to safety issues. For a user, it will take between 2 - 3 hours to collect the necessary information and add/submit the project to the platform. Usually, it requires 1 - 2 rounds of review to get to the final approved version, where metadata details are added or the location of the data is further specified using correctly formatted URLs.
### URLs, references and further information
[The PoDP platform](https://pairedomicsdata.bioinformatics.nl)
[The PoDP GitHub repository](https://github.com/iomega/paired-data-form)
[The PoDP publication](https://www.nature.com/articles/s41589-020-00724-z)
[The PoDP projects](https://zenodo.org/record/6403758#.Yk2WeS9m8_U) (downloaded >100 times)
[The PoDP web application in a zip](https://zenodo.org/record/6091663#.Yk2WfS9m8_U)
[Tool](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008920) that integrated the PoDP platform and used validated entities therein
---
title: "Lighthouse Award 2022"
author: "Annika Tensi"
date: '2022-03-16'
url: /lighthouse2022/
---
# Win the first Open Science Lighthouse Award
|<div style="width:250px"></div> | <div style="width:150px"></div> |
| -----------| ----------- |
| With the Open Science Lighthouse Award, we want to celebrate and reward WUR researchers and researchers from associated institutes (e.g., NIOO-KNAW) who have used open practices and tools to make their research more transparent, accessible and reproducible. <br> <br> We hope that the Open Science success stories of WUR researchers encourage more colleagues to open their research and promote the bottom-up adoption of open science practices across the science groups and research institutes. |![Lighthouse with text: Win the first Open Science Lighthouse Award](/images/lighthouse_txt.jpg) |
## Submission is closed
You can either submit your own Open Science case story to apply for the Lighthouse Award or you can nominate a colleague. There are two separate submission forms. Submission is open for students, researchers and support staff on all levels.
### **Closing date for submission: 25 April 2022**
## Present your case at the OSC-W launch event
The researcher with the most compelling, eye-opening or provocative Open Science story receives the first Open Science Lighthouse Award! All eligible submissions have the chance to present their case at the festive Open Science Community Wageningen (OSC-W) launch event in May (10 min presentation). All eligible case studies will be given public attention through the OSC-W Website.
## What are we looking for
Whether it is engaging with open research workflows and pre-registering experiments, sharing data and code, being involved in citizen science and communicating with stakeholders, or adopting other exemplary open science practices, we are looking for researchers who make open science part of their daily practice. We invite researchers to consider their full research life cycles and outputs in all possible forms, including papers, data, software and hardware, methods and infrastructure.
---
title: 'Special Nomination: Mangala Srinivas'
author: "Annika Tensi"
output: html_document
date: '2022-06-03'
---
*by Christine Jansen*
### Please describe why you think your colleague deserves the first Open Science Lighthouse Award
Open Science (OS) really came into the spotlight in Europe with the implementation of Plan S. While there is no doubt about the need and benefits of OS, it takes time to switch from the traditional rewarding in science which is strongly embedded in current tenure tracks to rewards based on sharing and openness. Mangala Srinivas has been working for several years, to promote OS, and to ensure that the necessary changes to the assessment criteria for researchers occur (Recognition and Rewards, R&R). Mangala was able to really push this agenda through her role as Chair of the Young Academy of Europe (YAE). Mangala was part of a keynote panel discussion at the release of the new R&R strategy by the VSNU and EUA, at the launch of their white paper “Room for everyone’s talent” in 2019 (1). The key point she made was that researchers cannot be assessed by current standards (particularly journal impact factors) while also being required to make their research open as this
puts them in an untenable position. In the same year, Mangala released a statement, together with EuroDoc and the Marie Curie Alumni Association to this effect (2,3). She also delivered a keynote address at a joint event on Plan S, organised by the Academia Europaea and KU Leuven (4), on “The Future of Research”. In 2020, Mangala participated in the Regional Consultation on Open Science for Western Europe and North America by UNESCO (5), again encouraging changes in the R&R to allow for more OS. After joining WUR in May 2021 as Chair of CBI (Cellbiology & Immunology group), Mangala has published 2 further articles in Nature on the urgent need for change (2021, Why science needs a
new R&R system(6)), and the need for adapting the current R&R schemes to encourage diversity (together with the Wageningen Young Academy, in press).
The data for her 2021 Nature article was published in Open Research Europe (ORE) as a Data Note (7) to allow broad access to the (anonymised) data.
Mangala is on the Scientific Advisory Board of ORE (8), and was recently interviewed for an article commemorating the 1-year anniversary of ORE in the EC magazine, Horizon(9). She stressed that although platforms like the ORE are essential, they will not be widely accepted until they are indexed in academic search engines like PubMed or Google Scholar.
Mangala stimulated the implementation of a comprehensive Data Management Plan (DMP) at CBI, together with other colleagues. The DMP emphasizes FAIR data and accountability, while promoting working with collaborators, both private and public. This has a direct impact on the way data is structured and managed within CBI. Translating a DMP to practical use and action on the ground is a challenge that she, and others at CBI, are now tackling.
Overall, Mangala has been working to promote OS for years now, while working to ensure that it does not disadvantage vulnerable researchers. I would like to recommend her for this award.
### URLs, references and further information
[1.](https://www.youtube.com/watch?v=YTXMt8tffQg)
[2.](http://eurodoc.net/implementation-plan-s.pdf)
[3.](http://www.eurodoc.net/news/2019/euinvestinknowledge-researchers-calls-on-national-governments-ineurope-to-protect-eu)
[4.](https://yacadeuro.org/tag/plan-s/)
[5.](https://en.unesco.org/science-sustainable-future/open-science/regional-consultations/westerneuropean-north-america)
[6.](https://www-nature-com.ezproxy.library.wur.nl/articles/d41586-021-01952-6)
[7.](https://open-research-europe.ec.europa.eu/articles/1-138)
[8.](https://think.f1000research.com/open-research-europe-submission/scientific-advisory-board/?utm_source=CPB&utm_medium=cms&utm_campaign=JQC19228#)
[9.](https://ec.europa.eu/research-and-innovation/en/horizon-magazine/open-science-publishing-strikes-richseam-ore-publishing-platform)
---
title: 'Submission Lighthouse Award 2022'
author: "Annika Tensi"
output: html_document
date: '2022-06-02'
---
# Yizhou Ma
## Open-source software development to accelerate adoption of 3D food printing
### Open Science Objectives & Practices
My projects aim to develop open-source software packages and publish open-assess journal articles to accelerate the adoption of 3D food printing as an emerging food processing technique. Specifically, I publish datasets with the FAIR data principles, host open-source software codes on the WUR GitLab repository, and record software demos on YouTube.
### Introduction
In my PhD thesis research, I develop a library of software packages to monitor and control 3D printing of foods.
I have published 1 open-access journal article with the dataset and analysis codes publicly available through the WUR's GitLab repository. The repository comes with a README file that allows others to reproduce my study results, reuse the scripts for new data, and perform secondary analysis on my dataset.
I have another under-review manuscript with the intent to publish with open assess. Together with the manuscript, we host another GitLab repository for an open-source software. The software is developed under the Creative Commons license and has been used by another collaboration project between WUR and Technical University of Eindhoven. I also recorded a demo video to help others use the software.
In the pipeline, I have another open-source software that has been tested internally in the Food Process Engineering group. This software is currently hosted on an internal GitLab repository with the intent to be open-source once the development is finished.
### Motivation
For me, open science is not a choice but the norm. During my studies, I have been benefited very much from open-source software and open science. It is fair to say that I "grew up" with open science. I'm fully immersed with the open science practices, so it is only logical for me to do the same and contribute the same to the scientific community.
To address the question, my study results are only meaningful if others are using them. To best help others to use my outcomes, I prepare everything based on the open-science practices. Because the 3D food printing community is still at its infancy, other developers and equipment manufacturers can directly adapt my software and solutions to their productions, accelerating the technological adoption of 3D food printing.
The concept of my project also extends to other food manufacturing practices, so making my methods and data open-source will help future researchers to implement similar solutions. Seeing others using my work and learn from my mistakes is fulfilling to me.
### Lessons learned
It is important to get permissions and supports from supervisors and other project stakeholders before implementing the open-science practices. We should have a clear list of outcomes on top of the traditional practice (normally just one manuscript). The list of outcomes can be annotated software scripts, tutorial videos, labelled and well-noted datasets, etc. We need to set the expectations beforehand and get all hands on deck.
Open science indeed comes with a price in terms of time and resources. We had technical difficulties for properly setting up GitLab through the WUR network infrastructure. Now we have a troubleshoot document to continuously improve our workflow with open-source programming.
I took the data management course from Wageningen Data Competency Center, and it was a great overview of available resources to achieve open science at WUR. I recommend researchers to take that course.
### How much extra time did the open practices require?
About 20% overhead on top of the regular time required
### URLs, references and further information
[Open access publication](https://www.sciencedirect.com/science/article/pii/S146685642100165X)
Open-source GitLab repositories:
[1](https://git.wur.nl/yizhou.ma/food-extrudability-assessment-and-prediction)
[2](https://git.wur.nl/yizhou.ma/extrusion-flow-tracker)
\ No newline at end of file
---
title: "Lighthouse Award 2022"
title: "Lighthouse Award"
author: "Annika Tensi"
date: '2022-03-15'
date: '2022-06-03'
url: /lighthouse/
---
# Win the first Open Science Lighthouse Award
|<div style="width:250px"></div> | <div style="width:150px"></div> |
| -----------| ----------- |
| With the Open Science Lighthouse Award, we want to celebrate and reward WUR researchers and researchers from associated institutes (e.g., NIOO-KNAW) who have used open practices and tools to make their research more transparent, accessible and reproducible. <br> <br> We hope that the Open Science success stories of WUR researchers encourage more colleagues to open their research and promote the bottom-up adoption of open science practices across the science groups and research institutes. |![Lighthouse with text: Win the first Open Science Lighthouse Award](/images/lighthouse_txt.jpg) |
| |<div style="width:1px"></div>| <div style="width:120px"></div> |
| ----------- |-| ----------- |
|With the Open Science Lighthouse Award, we want to celebrate and reward WUR researchers and researchers from associated institutes (e.g., NIOO-KNAW) who have used open practices and tools to make their research more transparent, accessible and reproducible.| | ![Animation of 3D printed white lighthouse with blue base](/images/award.png)|
## Submission is closed
You can either submit your own Open Science case story to apply for the Lighthouse Award or you can nominate a colleague. There are two separate submission forms. Submission is open for students, researchers and support staff on all levels.
We hope that the Open Science success stories of WUR researchers encourage more colleagues to open their research and promote the bottom-up adoption of open science practices across the science groups and research institutes.
### **Closing date for submission: 25 April 2022**
## Present your case at the OSC-W launch event
The researcher with the most compelling, eye-opening or provocative Open Science story receives the first Open Science Lighthouse Award! All eligible submissions have the chance to present their case at the festive Open Science Community Wageningen (OSC-W) launch event in May (10 min presentation). All eligible case studies will be given public attention through the OSC-W Website.
## What are we looking for
Whether it is engaging with open research workflows and pre-registering experiments, sharing data and code, being involved in citizen science and communicating with stakeholders, or adopting other exemplary open science practices, we are looking for researchers who make open science part of their daily practice. We invite researchers to consider their full research life cycles and outputs in all possible forms, including papers, data, software and hardware, methods and infrastructure.
Whether it is engaging with open research workflows and pre-registering experiments, sharing data and code, being involved in citizen science and communicating with stakeholders, or adopting other exemplary open science practices, with the Lighthouse Award, we prise researchers who make open science part of their daily practice. We invite researchers to consider their full research life cycles and outputs in all possible forms, including papers, data, software and hardware, methods and infrastructure.
You can find further information on the submissions 2022 below.
\ No newline at end of file
---
title: "Launch Event 2022 - Gallery"
author: "Annika Tensi"
date: '2022-06-03'
---
{{< gallery >}}
{{< figure link="/launch/1_OSCWlaunch.jpg" caption="Welcome" >}}
{{< figure link="/launch/2_opening.jpg" caption="Opening" >}}
{{< figure link="/launch/3_presentationVittorio.jpg" caption="Presentation Vittorio" >}}
{{< figure link="/launch/4_presentationEdo.jpg" caption="Presentation Edoardo" >}}
{{< figure link="/launch/5_presentationEdo.jpg" caption="Presentation Edoardo" >}}
{{< figure link="/launch/6_IntroElisabeth.jpg" caption="Introduction Elisabeth Bik" >}}
{{< figure link="/launch/7_IntroElisabeth.jpg" caption="Introduction Elisabeth Bik" >}}
{{< figure link="/launch/8_presentationElisabeth.jpg" caption="Presentation Elisabeth Bik" >}}
{{< figure link="/launch/09_awardJustin.jpg" caption="Award Justin" >}}
{{< figure link="/launch/10_presentationJustin.jpg" caption="Presentation Justin" >}}
{{< figure link="/launch/11_presentationJustin.jpg" caption="Presentation Justin" >}}
{{< figure link="/launch/12_OSCW core.jpg" caption="OSC-W" >}}
{{< figure link="/launch/13_reception.jpg" caption="Reception" >}}
{{< figure link="/launch/14_reception.jpg" caption="Reception" >}}
{{< /gallery >}}
\ No newline at end of file
......@@ -15,3 +15,5 @@ categories: null
# OSC-W Events
We are organising regular events at WUR and in collaboration with other institutes, OSCs and initiatives. Here you find an overview of upcoming and past events.
Please click on the events below for further information on the date and time, location and for signing-up.
---
title: "Lunch Seminar by Yizhou Ma"
author: "Annika Tensi"
date: "2022-06-03"
---
# **15 September 2022** **12.30 - 13.30 hrs**
*location will be announced soon*
# Sign-up link will be available in due time
During this lunch seminar, Yizhou Ma will present his open-source software development project on 3D food printing. Further information can be found [here](/award/yizhou_open-source/) and will follow soon.
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