eScience Center Fellowship Kick-Off Day

# eScience Center Fellowship Kick-Off Day Welcome, eScience Center Fellows 2023-2024!! [This document](tinyurl.com/nlesc-fellows23) is synchronized as you type, so that everyone viewing this page sees the same text. ## :clipboard: Code of Conduct Attendees are expected to follow those guidelines: * Use welcoming and inclusive language. * Be respectful of different viewpoints and experiences. * Gracefully accept constructive criticism. * Focus on what is best for the community. * Show courtesy and respect towards other community members. ## 🗓️ Agenda | 7 June 2023 | | |-|-| |10:30| Arrival and coffee ||--Plenary morning schedule--| |11:00| **Welcome and introduction to the kickoff day** - Lieke de Boer, Fellowship Coordinator |11:15|**Special interest groups (SIGs)** [slides](https://nlesc.sharepoint.com/:p:/s/FellowshipProgramme/EZdlA6mVrwdOugRxsiJt4NEBynBEa_OSvoR0dz3RL-esYQ?e=23VrrG) |12:00| **Administrative information** [slides](https://nlesc.sharepoint.com/:p:/s/FellowshipProgramme/EUXielYd-rpNqzBMMEqPd44BSGCFnQ2PT1ZBAVV6yIMA8g?e=6sOf4m) |12:30 | Lunch ||--Interactive afternoon schedule--| |13:30 | **Meet the Mentors** (and Fellows) [slides](https://nlesc.sharepoint.com/:p:/s/FellowshipProgramme/EYuGrHeO6OxLtzc2shd97-4B1diD-dv6MKjT0bMA1-9bWw?e=PU0vOw) | 15:00 | Coffee break | 15:15 | **Co-working session** (theme 1) [notes](https://hackmd.io/sF_mSKyvRa-AURBtHpMQOw?both#-Session-1-1515---1600) | 16:00 | **Co-working session** (theme 2) [notes](https://hackmd.io/sF_mSKyvRa-AURBtHpMQOw?both#-Session-2-1615---1700) | 17:00 | **Wrap-up and feedback** ||Evening schedule| | 17:30 | Dinner at [de Polder](https://www.cafe-restaurantpolder.nl/) ([6 min walk from the Center](https://www.google.com/maps/dir/Netherlands+eScience+Center,+Science+Park+140,+1098+XG+Amsterdam,+Netherlands/Cafe+Restaurant+Polder,+Science+Park,+Amsterdam/@52.3555563,4.9537807,18z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x47c609445d254f73:0x7c1ae2f2d3375410!2m2!1d4.9568783!2d52.356719!1m5!1m1!1s0x47c609434affb515:0x28f550585e142b29!2m2!1d4.9526319!2d52.3546622!3e2)) mintEMU - The Legacy of the European Postgraduate Master in Urbanism at TU Delft: A Text Mining Approach ### Room finder (3rd floor, Matrix III building): ![](https://i.imgur.com/jZClzqm.jpg) The plenary sessions are in Observatory / Telescope. ## Sign up for SIGs 1) Analytics * Meron * Diana * Mirko * Sven 2) Soft Skills * Serena * Meron * Thomas * Alexei * Funda * Francien 3) Data * Diana * Serena * Funda * Raoul * Alexei * Katharina 5) Machine Learning * Serena * Diana * Funda * Raoul * Katharina * Sven 6) Natural Language Processing * Serena * Raoul * Gabriele 8) UX-Web * Meron * Serena * Francien * Funda * Alexei 9) Science communication (contact: p.rodriguez-sanchez@esciencecenter.nl) * Serena * Funda * Francien * Alexei * Diana * Katharina * Thomas * Meron 10) Software sustainability * Thomas * Meron * Diana * Serena * Francien * Raoul * Katharina * Sven ## 👩‍💻🎓 Fellowship Coordination team Carlos Martinez-Ortiz, Lieke de Boer Contact us at fellowship@esciencecenter.nl Operations address: operations@esciencecenter.nl ## :question: Questions? ## Mentor-Fellow pairs and co-working session groups [GitHub discussions forum](https://github.com/orgs/eScience-Center-Fellowship/discussions) | Github username | Fellow | Mentor|Co-working session 1 group | Co-working session 2 group | |-|-|-|-|-| | solmyr1980 :+1: | Alexei | Mateusz Kuzak | SSH | Training materials | | | Ammar | Abel Siqueira | Not present | Not present | | diiobo :+1: | Diana | Hector Cadavid | Life science | Good practices 2 | | fgbossema :+1: | Francien | Valentina Azzara | SSH | Good practices 1 | | neurofunda :+1: | Funda | Eva Viviani | SSH | Training materials | | [gsarti](https://github.com/gsarti) :+1: | Gabriele | Carsten Schnober | SSH | Community engagement | | joshuadijksman :+1: | Joshua | Luisa Orozco | Cross-domain | Training materials | | kathiwaury :+1: | Katharina | Giulia Grocioni | Life science | Community engagement | | meronvermaas :+1: | Meron | Ewan Cahen | Cross-domain | Good practices 2 | | mirkosignorelli :+1: | Mirko | Barbara Vreede | Software development | Good practices 2 | | qubixes :+1: | Raoul | Djura Smits | Cross-domain | Good practices 1 | | [SereDef](https://github.com/SereDef) :+1:| Serena | Walter Baccinelli | Software development | Community engagement | | [sbte](https://github.com/sbte) :+1: | Sven | Lourens Veen | Software development | Community engagement | | tpronk :+1: | Thomas | Maaike de Jong | Life science | Good practices 1 | ## Fellows and their projects: [Short descriptions (please edit your own)](https://nlesc.sharepoint.com/:w:/s/FellowshipProgramme/EZyJ-VuLAktEg16nsGDGhugBFsOfjnq3TjCL2AbCcXzrSw?e=Z9uJza) ## :t-rex: Co-working sessions (15:15 - 16:15) These sessions are meant for everyone to learn from each other's experience. After these sessions, you can hopefully start your Fellowship project with some extra insights, and know how to help each other move forward. There may be different levels of proficiency and experience in the group, so try to avoid using jargon specific to your field. ## :computer: Session 1 ### Group 1: **SSH** (Cloud chamber :cloud:) * Alexei * Francien * Funda * Gabriele You're assigned to this group because all of your projects involve some connection to humanities and social sciences. Make a round, answering the following questions about your project, and writing down the answers in this doc: 1. What area of SSH is more closely related to your project? Funda- Behavioral and neurosciences Francien - Art Gabriele - Linguistics Alexei - linguistics and antiquity and archeology, economics, political science, psychology 2. What are the similarities and differences between your project compared to others? Funda & Alexei - educational & dissemination Francien & Gabriele - more development 3. What are the main challenges your project faces in this domain? There is a gap between people who develop and who use scientific softwares. Bridging the two groups or transitioning them from being a user to become developers or become frequent users, overcoming resistance of layman would be our eventual aim. 4. Which of your challenges match those of others in your group? Can you address anyone else's with resources or experience you have? Feel free to include links to resources. - Resistance of students who signed up for a course but had to learn softwares throughout their training. - Limited stakeholders using the sotware and figuring out ways to reach out to these niche groups. 5. Take a moment to think about what you can take away from the conversation to your own project. - 'Putting people out of their social scientist mental state' and prepare them mentally that they could be great programers, that technical skills could be acquired later in life. Idea of solution: invite such role models (social scientists turned into researchers using technical skills) as speakers during the project. - Finding challenges along the way. This could create a community in the long term. - Communication problems are common regardless of the research field. (Minutes by: Funda) (Please find the room for your next session by 16:15) *Notes go here* ### Group 2: **Life sciences** (Observatory) * Diana * Katharina * Thomas You're assigned to this group because all of your projects are related to life sciences. Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What area of life sciences is more closely related to your project? *For Diana, clinical neuroscience and neuroimaging. For Katharina, bioinformatics and biomarker development. For Thomas, medical science.* 2. What are the similarities and differences between your project compared to others? *Similarities: . Differences:* 4. What are the main challenges your project faces in this domain? 5. Which of your challenges match those of others in your group? Can you address anyone else’s with resources or experience you have? Feel free to include links to resources. 6. Take a moment to think about what you can take away from the conversation into your own project. Both Diana and Katharina work in R. All three want to organize a workshop/meetup, and are concerned with Software Sustainability. Differences are privacy issues (present with Diana), issues in the gap between bioinformaticists and biomarker researchers (present with Katharina),and the type of software (software in support of producible studies for Diana and multi-study software for Katharina, both for Thomas). We can collaborate on the software sustainability aspect as this is a shared concern. (Please find the room for your next session by 16:15) *Notes go here* ### Group 3: **Cross-domain** (Telescope) * Joshua * Meron (not attending) * Raoul You're assigned to this group because all of your projects are related to technologies that can be used across multiple domains. Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What domains can benefit from technology used in your project? 2. To what extent do the domains you are reaching overlap with other projects in your group? 3. What are the main challenges your project faces in this domain? 4. Which of your challenges match those of others in your group? Can you address anyone else’s with resources or experience you have? Feel free to include links to resources. 5. Take a moment to think about what you can take away from the conversation into your own project. (Please find the room for your next session by 16:15) Note taker: Joshua Refreshing memory Raoul: organizing workshops for researchers (diverse, geoscience, across university) to improve their workflows in software development. Documentation is not the focus; the point is more to introduce users to the existence of different types of workflows out there. Refreshing memory Joshua: developing Massive Open Online Course (set of Youtube videos :P) elements to train users across domains in the usage of Discrete Element Method (DEM) simulations for particle-based materials science. Raoul 1: Bioinformatics is already familiar with workflows, otherwise every domain can use it. Joshua 1: DEM methods are used in various domains such as pharma, civil, mechanical engineering, but can be used in places like foods/agrotech/battery/ceramics engineering if DEM methods are appropriately developed. Raoul/Joshua 2: Joshua's set is part of Raoul's superset. This is interesting because DEM methods also use or should use proper workflows. Raoul 3: one main challenge is barrier to entry in the use of workflows (Git, etc) - people have to learn many tools whereas they want to do research. Another challenge is the double issue of finding users who can be convinced of the virtues of workflows. Joshua 3: main challenge is barriers to entry DEM: there are many bells and whistles to learn/know/figure out before you can use let alone trust your code. Raoul/Joshua 4: LAck of domain knowledge among us is a small hurdle; the eScienceCenter can contribute here. Furthermore, in the applications of our Fellowship poducts, convincing users that the developed methods/course can bring them value is a core challenge for both of us. The methods / products developed by Raoul can definitely be used in a DEM MOOC context as well. Raoul/Joshua 5: we have common colleagues and interests! Raoul was positively surprised by meeting someone who is already curious about his work. Joshua is happy to find someone with whom he can effectively collaborate. ### Group 4: **Software development** (Cyclotron) * Mirko * Serena * Sven You're assigned to this group because your projects include further software development of software you have worked on already. Within the group, your software will be in different stages of maturity. Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What kind of software are you developing? What does it do? * Sven: climate/ocean models are very time-consuming to run, even on supercomputers. Sven's software runs in Python (instead of Fortran and C++) and should make it easier for PhD students to take over previous code * Serena: database with heterogeneous data sources collected over 20 years. Software tries to query data and metadata * Mirko: package for observational studies or clinical trials with survival outcomes, you typically follow participants over time to improve predictins but makes it possible to make predictions with many (~100) longitudinal variables. 2. What language is it written in? * Sven: Python * Serena: backend Python, interface R (Shiny) * Mirko: R 3. How mature is it? * Sven: Used already - rather mature * Serena: very green * Mirko: rather mature - already working but needs improving on internal functions, write a software article 4. (If applicable) What prevents you from being able to release the software tomorrow? What are the most urgent things you need? * Sven: change package name, automatic generation of documentation * Serena: hard to automate, very messy - lack of standards (e.g. variable names) * Mirko: NA (already available on CRAN) 5. What are the similarities and differences between the different kinds of software planned in your projects? * Similarities: some common languages, trying to make someone else's life easier (while often people make software just to get a paper published), sustainability * Differences: the rest 6. What needs match the needs of your group mates? Do you have resources or experience that can address anyone else's needs? Feel free to include links to resources. * Sven: * Serena: * Mirko: 7. Take a moment to think about what you can take away from the conversation into your own project. * Sven: * Serena: * Mirko: (Please find the room for your next session by 16:15) *Notes go here* ## :pencil: Session 2 (16:15 - 17:00) ### Group 1: **Community Engagement** (Cloud Chamber):cloud: [link](https://teams.microsoft.com/l/meetup-join/19%3ameeting_N2FlMDU0NWMtODcwNi00MzZhLWE4MmUtOTg2Mjk3OGNjNTcy%40thread.v2/0?context=%7b%22Tid%22%3a%22aa3aeacc-6307-42b2-ac05-787dd5c32574%22%2c%22Oid%22%3a%224cd51eb9-54ac-406c-8d37-41bfcac6970c%22%7d) * Gabriele * Katharina * Serena * Sven You're assigned to this group because your projects include building or expanding a community around research software or good research software practices. Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What are the activities you are planning? - Gabriele: conference attendance, set up an online communication platform (e.g. Slack, Discord) for users - Katharina: Organize 2 workshops, 1 before tool development to compare different existing tools and identify pain points, 1 after tool development to see how they interact with it, follow collaborative software development principles. - Serena: Demo recording, organize workshops to try out the tool, collect feedback and encourage people to adopt a proactive approach to software development to solve repetitive issues. - Sven: Organize 2 workshops aimed at convincing researchers of the importance of automated testing, open sourcing materials and code readability (which does not imply slowness). 2. Identify your community. Who would you like to reach? What is the (desired) size of your community? - Gabriele: NLP Interpretability researchers and researchers in AI bias and fairness - Katharina: Bioinformaticians working on biomarkers development and possibly non-bioinformaticians interested in the topic - Serena: Researchers in the biomedical field - Sven: PhDs and researchers building models to be run in parallel across multiple computing nodes, and students doing a course related to the code. 3. What proportion of the community are you currently reaching? - Gabriele: Not sure how many user there are currently (was presented to 100s of users, maybe 10-20 using it actively) - Katharina: The local community and personal contacts (one research group) expressed interested in using more bioinformatics during assay development and the tool once it will be available. - Serena: Currently being used in the same institution by some people. - Sven: The tool was used in a course for the past 3 years, with several people external to the organization reaching out via email to discuss tool design choices. 4. What (if any) are the main obstacles standing in the way of reaching those within your desired community? - Gabriele: bias against PhD student developed tool compared to more established institutions or companies working in the same domain, lazyness to learn new tools - Katharina: unwillingness to invest time to learn a new tool before gaining advantage from using bioinformatics software - Serena: Even if the tool doesn't require much learning upfront, people that are less code-savy are unwilling to learn how to operate it - Sven: People are not convinced that climate research conducted using the tool is meaningful, need for convincing proof of validity 5. Which (if any) obstacles have you already overcome in building, expanding and activating that community? How did you overcome them? Do you have examples of practical situations? - Gabriele: Getting users more involved in the tool with case studies and becoming part of the design process. - Katharina: Collecting existing software in a review, helping users to get familiar with the tool helps them being more involved and willing to use it. - Serena: Getting access to the data was already challenging because of privacy issues of medical data - Sven: Convincing supervisors that building oper-source and sustainable software is not a waste of time -- only achieved by doing it. 6. How does your community compare to ones from the others in your group? - Gabriele: tech savvy, division between people familiar with methods and people interested in using them without needing much depth. - Katharina: unfamiliar ith using research software, difficult to understand what they struggle with from the bioinformatics perspective - Serena: general unfamiliarity with research software from the biomedical community - Sven: variety of users (from students to researchers with cluster computing experience), challenging to include everyone 7. Do you have tips for others in your group? - Gabriele - Katharina - Serena - Sven (Please return to Observatory / Telescope by 17:00) *Notes go here* ### Group 2: **Good practices 1** (Observatory) * Francien * Raoul * Thomas You're assigned to this group because your activities include building or expanding a community around research software or good research software practices. Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What are the activities you are planning? 2. How does your project increase (awareness of) good software practices among researchers? 3. What are the similarities and differences between the planned good practices related activities compared to others? 4. What are the most urgent things you need to achieve the goals in your project related to good practices? 5. Which needs around spreading good practices awareness match the needs of others in your group? Can you address anyone else's needs with resources or experience you have? Feel free to include links to resources. 6. Take a moment to think about what you can take away from the conversation into your own project. 7. (Last 15 minutes, all together) Look at the discussion of the other 3 people. Do you recognize similar themes? Are there things you had not discussed? (Please return to Observatory / Telescope by 17:00) ***1.** Francien will get consultancy from eScience Center for Software Sustainability and UI design, and will organize a workshop later on. Thomas will develop a workflow for producing SMPs and interview MDR-compliant developers. Raoul will learn about frameworks for reproducible workflows and organize two workshops and a hackaton.* ***2.** Francien will lead by example. Thomas will introduce SMPs. Raoul will promote reproducible code* ***3.** Francien has a crappy workflow to fix; she's a target audience of Raoul and Thomas. At first sight, the type of software focused on is subtly different between Raoul (software for a specific study) and Thomas (more general purpose research-software), but at later stage Thomas hopes to expand his SMPs to that as well.* ***4.** Francien most urgently needs to expand her own knowledge. Thomas needs to get a first wave of SMPs to actually be produced. Raoul needs to learn about workflows first and find motivated researchers with crappy but functional worfklows.* *5 to 7 has been covered adequately by our earlier brainstorming in pursuit of answering 1 to 4.* ### Group 3: **Good practices 2** (Telescope) * Diana * Meron * Mirko You're assigned to this group because your activities include building or expanding a community around research software or good research software practices. x Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What are the activities you are planning? * Diana: organize a ReproHack event (mostly for PhD students) * Mirko: improve the infrastructure of a survival prediction package (R-based) - set up a github, documentation, examples, user-oriented paper 3. How does your project increase (awareness of) good software practices among researchers? * Diana: the whole point of the project is for people to realize how much reproducibility is currently a problem and how much it needs to be worked on * Mirko: raise awareness within the research field of the importance of ensuring that statistical methods can actually be used by other people 5. What are the similarities and differences between the good practices related activities planned in your project compared to others? * Similarities: raising awareness on how code/software is "treated, valued and rewarded badly" and how much this needs to change * Differences: Mirko -> software, Diana -> event 7. What are the most urgent things you need to achieve the goals in your project related to good practices? * Diana: make time to actually starting to work on the project + get more people involved * Mirko: fixing the technical parts of the package that need improvement + start writing 9. Which needs around spreading good practices awareness match the needs of others in your group? Can you address anyone else's needs with resources or experience you have? Feel free to include links to resources. * NA - our projects have somewhat different scopes * But: Diana knows a lot about Alzheimer and Mirko's methods can be applied to Alzheimer, so there is overlap in terms of interests / possible collaborations 10. Take a moment to think about what you can take away from the conversation into your own project. * Diana: how I can also benefit from this project in my future career * Mirko: good to try to connect with people working on Alzheimer - strong potential for interdisciplinary collaborations 11. (Last 15 minutes, all together) Look at the discussion of the other 3 people. Do you recognize similar themes? Are there things you had not discussed? * Diana: * Mirko: (Please return to Observatory / Telescope by 17:00) *Notes go here* ### Group 4: **Training materials** (Cyclotron) * Alexei * Funda * Joshua You're assigned to this group because your activities include giving training or developing training materials. Assign a note taker. Make a round where your first refresh each others memory about your proposed Fellowship activities. Then answer the following questions about your project, and writing down the answers in this doc. If it is not your turn, try to listen actively and ask clarifying questions or give suggestions. 1. What type of training materials are you planning to develop? 2. Can you find examples online of these kind of materials? Feel free to post links below. 3. What experience do you have in creating training materials? 4. What do you need to create successful training materials? 5. Are your ideas similar? What have you learned or can you learn from your group mates? (Please return to Observatory / Telescope by 17:00) *Notes go here* 1. MOOC; tutorials for software use; tutorials , datasets, workshops 2. https://www.wesleyan.edu/qac/summer.html 3. Multiple years of experience with course design including elements like knowledge clips, videos, workshops, etc. 4. Concrete learning objectives; constructively aligned components (objectives, activities, assessment); knowledge of the needs of your stakeholders (students) 5. Some of us learnt more about MOOCs. Others about (data and other) encounters across the curriculum. ## Final plenary session GitHub organisation is created: https://github.com/eScience-Center-Fellowship click tab "discussions" - Please fill out GitHub username in the table, we will add you to the organisation (please accept the invitation and "follow" the organization) - Have a look at your description in the file linked at the top of this document, I will paste it on the website tomorrow ## Feedback :+1: :-1: [Please fill out this survey](https://www.surveymonkey.com/r/CH6HV7T) Extra feedback from Francien: I like the photo session - it's nice to have a more professional photo both for the Escience center website that they are all similar, but also for us to use as personal photo's (i.e. on LinkedIn?) and when we advertise ourselves as Escience Center fellows (i.e. on a presentation).

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