2021 projects, #10: GSoC

Screenshot of https://summerofcode.withgoogle.com

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: 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.

Read more:
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

2021 projects, #5: community managers & resilience

The CMX holiday letter states: “ I just reviewed the data with the research team and one thing is crystal clear: community has become an irreplaceable part of business. In a year where a lot of businesses struggled, and there were many layoffs, community teams actually grew. And companies of all sizes, in all industries, are going to be investing in community in a big way next year.”

I have a standing alert for community-related position ads on LinkedIn, and see clearly a parallell increase in community positions offered in science & academia. Where ads earlier have been implicit about the community aspects, hiding it under terms such as ‘field knowledge’, nearly everyone knows and admits to some degree that in academia, it is impossible to succeed without community support. It is built into the system that your peers will (hopefully) acknowledge you and lift your work up – this mechanism is seen in such academic pillars as peer review, recommendation letters, and hiring committees, to name some examples.

Since I did my AAAS Community Fellowship in 2017, a training program that ran twice and which has now transformed into an independent organisation called CSCCE, Center for Scientific Collaboration and Community Engagement , I have been an active member in the community that surrounds CSCCE. We have a lot of interesting activites and projects around community management – interest groups (I’m in the Open Science SIG and lurking in the Diversity, Equity, Inclusion SIG), projects (I’m in one we started in 2017, aiming to describe and pin down community manager skillsets), and Working Groups (I’m in the Community Champions WG).

The theme for the 2021 Community Manager Advancement Day, which takes place on January 25, is resilience. A very fitting theme, after this Covid year. Resilience of self, when the world stops around you; resilience of communities to chaos and changes; resilience of organizations and society – where community has a huge part.

How do I become a “community-whatsit”?

This post was written when I was in the then AAAS CEFP training program, now CSCCE. It first appeared on the CSCCE blog on August 3, 2017. I am grateful to Lou Woodley (CSCCE) for edits and comments. The post was written in relation to my role as Community Engagement Officer at INCF (International Neuroinformatics Coordinating Facility).

“Don’t worry about understanding everything at once, NOBODY has the right background for this” said my MSc thesis supervisor, a dozen or so years ago. Then, the advice applied to mathematical modeling of the biochemical networks involved in learning and memory, an area that came with heaps of dense academic papers peppered with acronyms and incomprehensibly condensed descriptions of experimental protocols. Now, that advice applies equally well to community management, an area of expertise I did not even know existed in science until a few years ago.

With the ongoing funding crunch and uncertain academic job market, interest seems to be growing in alternative careers. As a person who went from a regular PhD to an atypical job at a science non-profit, I’m increasingly often asked for career advice that boils down to ‘What should I do to get to where you are now?’.

Recently I participated as mentor in a career workshop for postdocs and other students, and I was getting the same type of questions. Since I had no idea one could become a community manager, I ended up in my position mostly by a series of chance choices and events. But there are some things I am in retrospect glad I happened to do or learn, because they turned out to be very useful.

Should I get a PhD?

It depends. My PhD has been immensely useful, since I am still in a related community. If your intended community does research, or is close to science in some other way, having similar experience will help you understand them better, and will make it easier to talk their language. Joining a field shows you how it is to come into a community as a new member, and is a useful experience to have later when you are helping others become part of the community you manage.

Learning confidence in dealing with hard, perhaps unsolvable problems — like your own research project — is the very definition of a useful transferable skill. With that said, a PhD is also several years of niche work that will be hard to bear if you don’t love it (at least part of the time). And there is an inordinate amount of time spent formatting reference lists.

Should I learn something else?

Besides the content of your PhD? Definitely. I began my random walk towards community management with communication, and that is probably a good starting point if you have a background in research. If you are coming directly from academia, chances are you’ve become an expert at communicating clearly with your scholarly peers but are getting increasingly blank stares from anyone else. Or you might be a communication genius, but unless you have some way to prove that, many people will assume the incomprehensible scholar stereotype applies to you, too.

Science just published a great article on whether you should add another degree after your PhD and as they say, adding verified experience can help. But it doesn’t have to be formal courses. Writing a blog or running a podcast/YouTube channel/improv theater troupe will not only give you experience in communicating with a varied range of audiences. It will also serve as a handy track record of communicative ability. A general familiarity with social media will also be useful; if you are not working with it yourself, you will likely collaborate with those who do. And any task involved in generating or framing content — such as editing, layout, print, photography, user experience design and website management — is a valuable potential community manager skill.

Is it less stressful?

This question tends to come from people having done at least one post-doc and looking with bleak disillusionment at a future that seems to mostly consist of writing rejected grant applications. The answer is: Nope. At best it is differently stressful. Instead of organizing your life around one big risky project with a well-thought-out plan, you’ll be juggling an untidy heap of lesser but more severely conflicting projects — the inaugural CEFP fellows motto of “We multi-task while multi-tasking” is only partly a joke — and will most likely see your plans evaporate into thin air on a weekly basis. And instead of not knowing what you are doing after your three years of funding run out, you’ll be subject to the vagaries of yearly or even quarterly budgets.

But I can’t find a job like that out there.

To which I say: Grow your job into the role you want! A lot of jobs border on potential community management roles. Mine was a traditional one-way communications job at the start. I did not plan to spend the rest of my life writing newsletters and layouting print materials, and I also felt that we as an organization could probably serve our community better if we were a bit more communicative.

So I asked my boss to let me start a few social media efforts in our organization’s name, beginning with Twitter. I went to conferences and talked, talked, talked to everyone who was introduced to me as a community member, trying to find out what they wanted and needed. I got involved with a few community initiatives, some that worked and some that didn’t, and spent hours trying to pinpoint what made some take off while the others simply puttered along. I organized boring workshops and interesting workshops, and tried to do the latter more and more often. Gradually, I began thinking more like a community manager, and less like a regular communications person.

All the major deciding points in putting me where I am today looked like random events at the time. There happened to be funding for a PhD position. On a whim, I started a blog. I was lucky to find a job where I could stretch my old role into a new one. Ask most other community managers, and I suspect they will look back at an equally random career trajectory.

So don’t worry. Nobody has the right background for this at the start 🙂

You can learn more about scientific community manager roles (including Malin’s!) in the CSCCE Meet a Scientific Community Manager series. Find all of the CEFP Fellows’ posts here.

This post was originally posted on the CSCCE blog on August 3, 2017.

How a blog snowballed into my current career

I started blogging science after a couple of months into my PhD, because I needed an outlet for all the fantastic papers I found that were ”not relevant” (to my studies and project). I had been reading author blogs (LiveJournal!) mostly, seen the odd blogging scientist now and then for a few years and figured ’Hey, I can probably do that!’. As it was early days, I hadn’t quite yet succumbed to the academia == English norm, so I wrote in Swedish. Unbeknownst to me at the time, that was like 3rd or 4th blog *in total* in Swedish focused on science. After a few years, I had built up enough of a presence to be invited to talk and write in other venues, including a summer stint as a ’real science journalist’ over the summer at one of Sweden’s biggest newspapers, Dagens Nyheter. I picked up some interesting friends during bloggin, including a food writer, and we two decided to apply for a book grant (I thought it was risk-free, we would not get it, because the one thing I knew about grants is that you don’t get them). But we did, and I had to go to my professor and say, ’Hey, I got a grant and will need to work part time on my PhD thesis’. He accepted. At that time my blogging dvindled to almost nothing, and I turned to Twitter instead (’it is a very short format, it won’t take much time’. Hah.).

So I wrote a book in parallell with my thesis work for about a year, spent some much needed time on Twitter whenever I got up for air, and at the same time my second mentor started working in something big and global I vaguely knew was about neuroscience, so I didn’t se her that often (that was INCF). I skimmed their web page occasionally to see what she was doing, and one time I came across an old job ad of theirs for a scientific communications officer, degree preferred, and with knowledge of neuroscience. I had learned from my journalist friends and acquaintances that hired positions in scicomm did basically not exist, and always had hundreds applying. So I asked offhand when we met next time, ‘How on earth did you not get anyone, and do you need help with anything urgent’? Long story short, the next week I had a talk with the project PI and got offered the job. So I went to my poor professor, AGAIN, and said ‘I want another 20% off my thesis work, because I accidentally got this other job…. And he accepted AGAIN, so then I did 20% book/20% INCF comms/60% thesis for another year, during which the book got finished and printed, INCF newsletters came out regularly, and the thesis got written. Then I took the weekend off, and started full-time at INCF next Monday (while still doing the occasional talk, interview or blog post on the book).

I still have a sort of parallel ‘career’ as a scicomm person, though mainly I’ve written for free for causes I like (the blog that became the book, for instance), and I mainly do my scicomm via Twitter. I’ve been on the Advisory Board for Poulär Astronomi (Popular Astronomy) since my blogging days. Right now, I am one of the Swedish members of an EU project called RETHINK, about improving scicomm (its Swedish Node is run by Vetenskap& Allmänhet). I also run a network, founded with some friends and friends-of-friends, for research communication professionals called FORSKOM (it lives on LinkedIn, and is officially bilingual Swe/Eng).

Community engagement working notes: monthly peer meeting

In 2017, I entered a AAAS Fellows program on Scientific Community Engagement, called “Community Engagement Fellowship Program” or in short, CEFP. The program has now moved to the Center for Scientific Collaboration and Community Engagement.

Group photo of 20 smiling people in blue tshirts, all 2017 community engagement program fellows.
The CEFP 2017 Fellows, photo by permission of Lou Woodley. I’m in the middle row at the left.

This program was a turning point for me, personally and professionally. Many of us still keep in contact, and one of the things I regularly do is meeting virtually with another CEFP fellow, Stefanie Butland. She’s in Canada and I am in Sweden, so we meet virtually over audio (for the bandwidth to keep up with us). I really recommend you to do something similar, if you are lucky enough to find a compatible person.

We meet the same day each month, and usually check in the day before to confirm the time or adjust it if necessary, and we always end the talk by confirming the next meeting time.

We use these talks mainly to ask for advice on challenging issues – for a while Stef talked about the same hard issue for months and it worked out! – and for celebrating achievements and successes. Several of the issues work themselves out while we are discussing them.

It works because we are strict about keeping to 15 minutes each. Usually, we self-regulate around our own 13-minute marks. Despite the short time, we can get a lot done, because we trust each other and are honest. And we both have similar and different experiences, good and bad, from our community manager work, so there is almost never the need to explain a lot of detail.

Andra länkar / other links

Min doktorsavhandling går att ladda ner från DIVA (länk)
Min licavhandling går också att ladda ner från DIVA (länk)

Jag gick ett träningsprogram (Fellow’s Program) via AAAS under 2017, för att utvecklas som community manager. Programmet har nu omformat sig till en fristående organisation, CSCCE (Center for Scientific Collaboration and Community Engagement) och man kan fortfarande bli en fellow. Och här är mina fellow members!

My PhD thesis can be downloaded from the DIVA portal (link)
My licentiate thesis can also be downloaded from the DIVA portal (link)

I was accepted to a training program for scientific community managers (Fellow’s Program) via AAAS in 2017, to develop further as community manager. The program is now reformed as CSCCE (Center for Scientific Collaboration and Community Engagement) and you can still become a fellow. And these are my fellow members!

Oroa dig inte, ingen har rätt bakgrund för det här från början – från Tidningen Curie

När jag och mina kollegor diskuterar med neuroforskare om vad de och fältet behöver slutar det ofta med att vi pratar om utbildning – främst av mastersstudenter och doktorander, men även av postdocs och mer seniora forskare som byter eller utökar sitt fält. Särskilt pressande verkar behovet vara för de som använder metoder som ger mycket data, eller som kräver rejäla kunskaper i både labbjobb och analys eller programmering – något som gäller allt fler. Neuroforskningen har utvecklats oerhört snabbt det senaste decenniet, med resulterande explosioner av metoder, stora datamängder och nya verktyg – och även eftersläp i utbildningsinnehåll. De lokala utbildningarnas innehåll ger ofta bara delar av den bakgrund som krävs, sedan får man lappa efter bästa förmåga med korta kurser, ofta i ett annat land, eller på egen hand försöka gissa vad man behöver veta och sedan hitta litteraturen.

Min egen doktorandutbildning i beräkningsbiologi (mer känt under det engelska namnet computational neuroscience) var precis ett sådant ihopkämpat lapptäcke av halvrelevanta universitetskurser – från både KTH, SU och KI – och djupdyk i forskningsartiklar och böcker, spetsat med ett par lätt surrealistiska veckor på kurs i sydligaste Polen, där jag framför allt lärde mig massor om metalloxidsensorer. ”Oroa dig inte”, sa min bihandledare godmodigt, ”ingen har rätt bakgrund för det här från början”. Jag hade tidvis varit beredd att ge min högra arm för ett lite mer balanserat och genomtänkt kurspaket, och jag kommer fortfarande ofta i kontakt med studenter som sitter fast i samma typ av pusslande. Nu har de dock även MOOCs, gratis föreläsningsvideor på youtube, helt webbsända konferenser, hundratals diskussionsforum och möjligheten att hitta medstudenter och mentorer via sociala medier… fast att hitta dessa utspridda resurser är ofta inte lätt, om man inte redan vet var man ska leta efter dem.

För några år sedan höll min organisation, INCF, tre workshops för att få en samlad syn på neurofältets utbildningsbehov. Workshop-rapporterna finns att läsa här, men en av de viktigaste slutsatserna är kort och enkel: man behöver börja tidigt i utbildningsstegen. Redan under masterutbildningen behöver biologerna få tillgång till matte, fysik och programmering, och fysikerna och matematikerna få tillämpa sina kunskaper på biologiska system, riktiga och modellerade celler och organ. På så vis får de en bredare samling verktyg att angripa problem med, lättare att samarbeta med folk från varierande bakgrunder, flera möjliga utbildningsvägar att fortsätta på, och flera kompetenser att bära med sig ut i forskning eller arbetsliv.

För varje sådan dubbelkompetent ny forskare får samhället också en bättre chans att lösa ett av vår tids stora hälsoproblem: att från djungler av data lista ut varför hjärnan fungerar eller slutar fungera. Ingen börjar med rätt bakgrund för det, men många fler skulle kunna ta sig hela vägen dit än som får chansen idag.

Det här är min sista post för Curie. Tack till er som läst! I fortsättningen hittar ni mig på Twitter och på min egen blogg.

Den här bloggposten publicerades från början 2014-09-24 på Malins gästblogg på Tidningen Curie.

En snart passerad sommar av kod – från Tidningen Curie

I sommar har över tusen studenter och nästan tvåhundra organisationer varit sysselsatta med att vidareutveckla öppen mjukvara inom Google Summer of Code; ett globalt program sponsrat av Google där studenter från hela världen får stipendier för att skriva kod åt olika öppna mjukvaruprojekt. Tretton av studenterna har jobbat med mentorer från olika neuro-relaterade forskningsprojekt och forskningsverktyg via min organisation (INCF), och jag och en kollega har rekryterat mentorerna, följt upp och rent allmänt stått för så mycket som möjligt av de administrativa bitarna. Igår, den 18:e augusti, var det officiellt sista dagen.

Det är vårt fjärde år som mentororganisation, och på många sätt ett fantastiskt kul projekt att jobba med. Studenterna är smarta, motiverade och entusiastiska över möjligheten att bidra till projekt och verktyg som behövs och gör nytta. Mentorerna får mycket utveckling gjord till priset av regelbundna mentorsinsatser, och projekten får nya deltagare – många fortsätter på ett eller annat sätt att involvera studenterna efter stipendieperiodens slut, eller plockar upp lovande studenter som precis inte kom igenom den kompetitiva delen där de mest lovande studenterna väljs ut. Vi som mentororganisation får glädjen att hjälpa vår community att hjälpa varandra; många av mjukvaruprojekten drivs helt eller delvis ofinansierat av forskarna som är involverade och vi vet hur många små hål det finns att täppa för att verktygen ska bli bättre, snabbare och smartare. Och alla förbättringar hamnar öppet tillgängliga för andra att plocka upp och spinna vidare på.

Tyvärr verkar den här möjligheten vara rätt okänd för många forskare och projekt. Det är synd. Kraven för att bli godkänd som mentororganisation är klart överkomliga, och många projekt som har plats för och nytta av exjobbare skulle kunna använda sig av det här initiativet för att nå ut till fler (och dessutom kunna betala dem en smula).

Förmodligen blir det en ny runda Google Summer of Code nästa år, beskedet brukar komma senast i januari. Om du har ett öppet mjukvaruprojekt som skulle ha nytta av fler händer på tangentborden, eller kommer i kontakt med studenter som vill prova på öppen mjukvaruutveckling, tipsa dem! Jag och min kollega svarar förstås även gärna på frågor om våra erfarenheter, bara att ställa dem i kommentarerna här nedan.

Läs mer:

Den här bloggposten publicerades från början på Malins gästblogg på Tidningen Curie.

Slutet för hårddisken i byrålådan? – från Tidningen Curie

I teorin kan jag lätt komma åt alla modeller, data och analysskript från mina år som doktorand. De ligger på hårddiskar, noggrant inpackade i antistatiska påsar, i byrålådan. Skulle jag behöva komma åt faktiska filer blir det svårare – dels ska diskarna fortfarande fungera, dels ska det gå att hitta och installera gamla versioner av programmen som kör modellerna eller läser in och analyserar mina data. Vissa filformat kan jag inte alls använda, eftersom mjukvaran som kör dem kräver en snordyr licens som jag inte längre har tillgång till. Än så länge kan vi nog kalla problemet med att nå mina data “svettigt men inte omöjligt”. Men om tio år? Tjugo? (Och om jag själv inte är tillgänglig då – kan någon annan alls förstå och återskapa det jag gjort?)

Deprimerande nog är jag långtifrån ensam. Så ser det ut lite överallt i den akademiska världen. En studie av tillgängligheten för data bakom drygt 500 biologiartiklar från ett och samma subfält, som publicerades i början av året, visar att data snabbt blir otillgängliga. Data från artiklar som publicerades 1991 gick bara att få tag på i en tredjedel av fallen – antingen var kontaktpersonerna omöjliga att få tag på, eller så låg data otillgängligt på avlägsna platser och i format som slutat fungera (minns ni zipdrive?). Även nya data var relativt svåra att få tag på, men då främst för att många tillfrågade inte ville dela med sig.

Datadelning är ett komplext problem med såväl tekniska som sociologiska aspekter, ibland även etiska och lagliga (särskilt inom det medicinska området). Trycket på att dela ökar, både från finansiärer och från tidskrifter, och det har flammat upp flera intressanta diskussioner i spåren av ändrade riktlinjer och krav (till exempel reaktionerna på PLoS ändrade datapolicy i början av året).

Personligen gillar jag principen att  göra data tillgängligt (senast) i samband med publikationen av en artikel. Tillgängliggörandet löser inte problemet med att kunna reproducera egna och andras resultat – ofta ligger det många analyssteg mellan data och resultat, och analysstegen kan vara svåra att replikera – men det tar bort de ”enkla” delarna av problemet: Data som blir onåbara för att en kontaktperson för länge sedan bytt jobb och mailadress, data som går upp i rök för att lagringsformat blir trasiga eller obsoleta.

Det gläder mig att möjligheten att publicera diverse sorters data formligen har exploderat under de sista åren, åtminstone inom mitt fält. Initiativ som Dryad och Figshare låter användare dela allt från figurer till kod och filer, unikt identifierbart och citerbart. Data kan publiceras som rena dataset med en DOI (DataCite), minipublikationer (t ex F1000 ResearchNotes) eller som hela papper (GigaScienceJournal of Neuroinformatics).  Till och med Nature har startat en datatidskrift. Det ska bli så intressant att se vad som händer de närmaste åren. Blir det här slutet för hårddisken i byrålådan?

Den här bloggposten publicerades från början 2014-06-02 på Malins gästblogg på Tidningen Curie.