I cancelled my pricey WordPress business plan and reverted my blog back to basic. Some things here might look weird a while.
10+ years of Brainhack: an open, inclusive culture for neuro tool developers at all levels
Brainhacks and similar formats are increasingly recognized as a new way of providing academic training and conducting research that extends traditional settings. There is a new paper out in Neuron, by 200+ authors, describing the format and what makes it valuable to the community. This post aims to highlight some of the core themes of the paper.
Brainhacks have been held since 2012, organized by local communities, sometimes in sync with other hackathons taking place elsewhere. In 2016 the format developed into the Brainhack Global – a synchronous swarm of hybrid meetings arranged by local communities with local and virtual participants. In 2020, during the pandemic, the BG went fully virtual.
Figure 1D from https://doi.org/10.1016/j.neuron.2021.04.001
A similar growth of hackathons has occurred in communities adjacent to Brainhack. INCF started funding hackathons early because our community asked for it; and when we saw the value and inspiration hackathons brought to the community, it became a regular line item in the INCF budget. Since funding our first hackathon in 2012, we have funded or partially funded at least one hackathon each year (see our entry in Acknowledgements).
The Brainhack format is inspired by the hackathon model and centers on ad-hoc, informal collaborations for building, updating and extending community software tools developed by the participants’ peers, with the goal to have functioning software by the end of the event. Unlike many hackathons, Brainhacks welcome participants from all disciplines and with any level of experience—from those who have never written a line of code to software developers and expert neuroscientists, and also feature informal dissemination of ongoing research through unconferences. Also unlike some traditional hackathons, Brainhacks do not have competitions. Brainhacks value education; recent major Brainhack events even have a TrainTrack, a set of entirely education-focused sessions that run in parallel with regular hacking on projects.
The five defining Brainhack features:
1) a project-oriented approach that fosters active participation and community-driven problem-solving
2) learning by doing, which enables participants to gain more intensive training, particularly in computational methods
3) training in open science and collaborative coding, which helps participants become more effective collaborators
4) focus on reproducibility, which leads to more robust scientific research; and
5) accelerated building and bridging of communities, which encourages inclusivity and seamless collaboration between researchers at different career stages
Brainhacks have increased insight in the value of tool usability and reusability and the need for long-term maintenance; shifting community culture from individuals creating tools for their own needs to a community actively contributing to an existing resource. They also help to disseminate good practices for writing code and documentation, ensuring code readability, using version control and licensing.
Brainhacks promote awareness of reproducible practices that integrate easily into research workflows, and show the value of data sharing and open data. They introduce participants to data standards, such as BIDS, allowing them to experience the benefits of a unified data organization and provides them with the skillset to use these formats in their own research.
Brainhacks create a scientific culture around open and standardized data, metadata, and methods, as well as detailed documentation and reporting.
The Brainhack community are currently also working to collate Brainhack-related insights and expertise into a Jupyter Book that will serve as a centralized set of resources for the community.
Brainhack: Developing a culture of open, inclusive, community-driven neuroscience
Det här inlägget skrevs för och publicerades först (12/5 2021) på INCF’s blogg
Lansering av nya Horisont Europa (10/2)
En hel dag, med några korta pauser, tog det att presentera grundpelare och huvudteman för det nya ramprogrammet för EU-forskning, Horisont Europa (#HorizonEurope). Presentationen arrangerades gemensamt av 6 stora svenska finansiärer; Energimyndigheten, FORMAS, Forte, Rymdstryrelsen, Vetenskapsrådet, och Vinnova. Många bra presentationer och panelsamtal! Jag har summerat det hela i tweets här, men det finns en del att lyfta upp som inte ryms i kortfattade meningar.
Öppen vetenskap nämndes EN gång (av John Tumpane, från FORMAS). Data-delning nämndes inte alls. Samverkan däremot nämndes upprepade gånger, framför allt med fokus på industrin. Standarder nämndes i förbifarten, framför allt som något viktigt för industrin att bevaka och delta i utvecklandet av.
Mycket av fokus låg på “partnerships”, arrangerade och finansierade strategiska multi-partssamarbeten som är menade att ge garanterad förutsägbar nytta. Hela 50% av budgeten går dit. Partnerships är inte nya för EU, men det utökade fokuset på nytta är en lite ändrad inriktning.
En nyhet för det här ramprogrammet är “missions“, övergripande målbilder som ska vara förankrade i samhällsbehov och ge samhällsnytta, och göra det lättare att nå målen för the European Green Deal och Europe’s Beating Cancer Plan såväl som hållbarhetsmålen.
Forskningsinfrastrukturer nämndes en hel del i början av samtalet (det är en av pelarna), och får en hyfsad andel av budgeten, men var inte särskilt närvarande när det kom till samverkans-diskussionen (där jag tycker de absolut passar in).
Regioner nämndes som möjliga innovationshubbar och koordinatorer, vilket var en trevlig ny vinkel – tidigare har jag mest hört regioner nämnas som trösklar och fragmentering, och ett problem för det svenska Life Science-ekosystemet.
Universitet nämndes i början – när vikten av rätt utbildning och mobilitet i utbildning diskuterades – men inte explicit i senare diskussioner om samverkan; där låg fokus mest på individuella forskare och på industrin. Universitet borde rimligen också vara nyckelmedlemmar i samverkansprojekt.
Två viktiga gap (”valleys of death”) i kunskapsöverföring och nyttogörande nämndes: den slingrande vägen som krävs för att ta forskning från labbet till industrin, och svårigheten att skala upp innovativa start-ups på ett hållbart sätt.
Regeringen håller på och arbetar ut en nationell strategi för Sveriges deltagande i Horisont Europa, det är dock ännu oklart exakt när den kommer vara klar. Det ska bli intressant att se vad den innehåller; EU-ansökningar anses allmänt vara tunga, arbetskrävande och komplicerade. Stödbidrag för att frigöra tid att sätta ihop en ansökan vore kanske användbart. Utökat stöd från universitetens administratörer och Grant Offices också. (När jag jobbade med mitt första EU-projekt hade vi en EU-kunnig administratör till hjälp, och vilken skillnad det gjorde).
Tydligen hade Norge sin motsvarande presentation redan i höstas.
Project update: GSoC
We (INCF) have, as of this morning, officially applied to Google as a mentoring organization in 2021. This is our 11th time. We have a Project Ideas list of 55 projects from 27 mentor teams, a new record!
The next step is interacting with prospective students, and waiting for Google’s announcement of this year’s accepted mentor organizations (March 9). Since a few years back, we post all project ideas on our forum to make it easier for students and mentors to discuss.
Project Gunhild update: finished!
Thick yarn makes for a quick knit. I am already finished with the Gunhild cardigan, a month before the agreed deadline. Slight stumbling block on the way; I ran out of main colour yarn after doing some modifications. And it wasn’t to be had anywhere in Europe, and out of stock at the supplier.
But I had bought some extra contrast color yarn, so I ended up doing half sleeves in the contrast color, and not just the edging. With extra long sleeves, which I like. And I sewed in a button so it would be wearable without a shawl pin for closure.
Project Gunhild update: blocking!
Knitting thick yarn is exponentially quicker than thin yarn, so I am already approaching done. Gunhild is knitted, steek-ed, and has edgings – just a soak, then blocking (persuading the knit fabric to reach its final intended shape).
There was one major setback on the way – I ran out of the main colour yarn after adding some much needed bust space. And so, it turns out, had every yarn store on the continent. That particular burnt orange nuance was backlisted months in 50 different yarn stores. I should in retrospect of course have gotten an extra ball of yarn of each color; I only got an extra ball of the gray contrast yarn. So this Gunhild is unique, with contrast coloured half sleeves, and slightly different edging.
Project update: Gunhild Cardigan
The needles finally arrived, a bit after Christmas. I have finished the yoke, and am now setting up for sleeves.
2021 projects, #10: GSoC
This is not a new project, by any means, rather one of my long-running favorite projects – the Google Summer of Code. INCF has partcipated each year since 2011, and I have been the main org admin on ONCF’s behalf for all but the two first years.
I described GSoC in some detail in Swedish back in 2014 when I guest-blogged at Tidningen Curie (“En snart passerad sommar av kod”). Many of the things I named as positive then are still true today; it is in many ways a fantastically fun project to work with. The students are smart, motivated and enthusiastic over having the possibility to contribute to projects and tools that are needed and useful. The mentors get a lot of development done for the price of regular mentoring, and the projects get new contributors – many continue to involve their students one way or another after the paid period, and some of them come back as mentors for the same project they started on. One former student, from 2018, is even my co-org-admin! (Hi, Arnab!) As mentoring organization, we get the joyous task of helping our community members help each other; many of the participating software tool projects are developed an maintained on small or no funds by the researchers themselves. We know how many small gaps there are that need to be bridged to make community tools better, faster, and smarter. And all the developed and inproved resources are openly accessible for everyone to pick up and continue working on or extend.
January, now, is the run up period – we have a call out for project suggestions and mentors, and responses have just started trickling in. Usually the mentors/project owners come to us with specific, well-thought-out and well described ideas, and sitting at the other end reading them all is a great experience – it is a veritable fountain of scientific and technical creativity, and one of the high points of my year. Projects that are well scoped and described – nearly all the submissions – end up on our official Project Ideas List and form the most important part of our application (I think, nobody knows exactly what Google looks for). As soon as that list goes public, around the end of January/start of February, mentors start interacting with potential students, working out the students’ project proposals. But slowly. The real explosion in activity comes when Google announces the year’s accepted organizations, this year that announcement goes out on March 9 (usually pretty late in the day, since it is on US-compatible time). It is always a very nervous day.
This year, Google has reshaped the program a bit, shortening the time spent coding and lowering the (high) threshold for participation. Which means we will get more students who are not hard core coders (yet) and need some support – which we as mentoring organization will be partly responsible for providing – and also the mentors and their community – all student projects start with an official community bonding period (genius idea). I distinctly remember being new to coding as a student, and hope that experience will help me be helpful.
2021 projects (9 and counting)
It seems I have a lot going on this coming year, I was a bit surprised myself when I started counting out my projects and landed at 9 long before I was done. Here is a status update:
2021 projects, #1: social media critique
I have the book, digital now and paper on the way, but have not started yet.
2021 projects, #2: Veganuary
Going well so far; veganizing breakfast was easy, quick work-from-home lunches depend mostly on what we ate the days before so they will veganize themselves in time. Dinner requires more adjustment, since I have two kids – relativley open to eating new things, but one of them is probably a supertaster. Most of my #veganuary updates will be posted on Instagram.
2021 projects, #3: test-knit a cardigan
Also going well, I have the yoke almost done. The only annoyance is my cable keeps unscrewing from the right hand needle, regardless of how hard I screw it stuck. Again and again.
2021 projects, #4: learn something new
This project hit an unanticipated rock in the road – the Swedish AI course I joined, “Elements of AI” in Swedish translation, which looked good at the start, turned out to be a disappointment. Weirdly formulated problem statements – I supposed they aimed to be inclusive give simple questions, but missed the mark – and finnicky automated-response-checkers. Translation was great, though. The only term not well translated was Data Scientist.
2021 projects, #5: community managers & resilience
Community managers at large have been a positive force for good, this year. In late January, there will be a Community Manager Appreciation Day, themed “resilience”. Expect some posts on that.
2021 projects, #6: scouting & leadership
We joined in late November, so the only scout meetings we have had so far took place on Zoom. But there are plans to be outside and DO things, which I look much forward to. And I am psyched to be a parent-leader; I have so many ideas for keeping the kids busy and entertained.
2021 projects, #7: books
This will be the most work, likely. All books in the apartment need to get sorted, a fair amount will be packed in boxes, and the equal amount of books will come up from the cellar storage. All books to be scanned and registered. And I need to go through, sort and tag all my 700 e-books.
2021 projects, #8: podcasts
This project, I think, will be a main contributor to keeping me sane. I plan to take long walks and listen to interesting things. I have already found a few new favourites to add to my listening rota (which so far is mainly EscapePod): the ORIONScience podcast, and the Svenskan i Samhället (Swedish in Society) podcast.
2021 projects, #9: RRIDs on everything
This is by far not my only upcoming work project. There will be Google Summer of Code, there will be INCF Working Groups, and literature search for the INCF Infrastructure Committee. And meeting new people, helping some people connect and collaborate… I will likely not have a boring moment.
2021 projects, #9: RRIDs on everything
This project is work-focused, but will surely frame my thinking and actions also beyond work. My latest work strategy meeting can pretty much be summed up in one sentence: RRIDs on everything (and if it doesn’t have an RRID yet, get one for it).
RRID is short for Research Resource ID, and is a type of identifier to inambiguously identify, mention and cite a research resource, taken broadly. Web portals, software tools, antibodies, cell/animal lines or bacterial strains. RRIDs grew out of the Research Resource Identification Initiative, whose key members also are part of the INCF community in the US, ands was launched as a recommendation in 2014, re-emphasized by successful trial results published in 2016.
If you have ever experienced an everyday name or identity collision – a similarly named classmate, a repeatedly mis-dialed phone number, getting emails meant for another person, having a neighbour or office colleague who gets your mail and you get theirs – you should already have a hunch about why identifiers are important, and what not having them means.
Simply put, identifiers give us a way to be more specific and precise than mere words can offer. There are existing identifiers for research papers (DOI:s, since old, ~2000s), people (ORCID:s, even older, Oct 2012), and research institutions (ROR in 2019, GRID in 2015). And since even longer, books have identifiers. ISBN, the International Standard Book Number, was published in 1970 as international standard ISO 2108. And identifiers typically are compact strings of characters, put together after a pattern, because you want them to be easy to use AND computer-readable .
But the existing set of identifiers did not cover all of research nearly enough: there were (and are still) problems with, for example: exactly and unambigously stating which antibod(ies) from which producer(s) you actually used. Or which breed of lab rat. Citing tools and specifying transparently which tools you use. Hence, RRIDs were conceived, and there is an ongoing campaign to get them broadly used.
Identifiers are useful on their own, but there are broader aspects – if you want to make science FAIR (Findable, Accessible, Internoperable, Reusable), identifiers will be a part of your toolset. They also need to be machine readable, because computers deal with thousands of data points a lot better than most humans do, and it would be nice to be able to automate identification and information gathering. They need to be persistent, i.e stay the same and not start meaning something different regardless of how tech develops. They also need to be resolveable – there needs to be a service at the other end, likely a database – storing the associated info.
The idea is, if everything has an RRID, it doesn’t matter if information is spread out like a box of dropped tooth picks all over the formal and informal scientific digital landscape in preprints, papers, posters, websites, blog posts, social media – it is still findable, as long as it is digital, attached to a PID, and available for indexing. So my mission is, simply, to find out which important-to-neuroinformatics research objects are not yet findable, and change that.
RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods
Using ORCID, DOI, and Other Open Identifiers in Research Evaluation
Unique, Persistent, Resolvable: Identifiers as the
Foundation of FAIR