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 and counting)

nature sky sunset the mountains
The sun setting on 2020. Pexels.com

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.

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

Project Veganuary: beginnings

vegan gyros with vegetables
Vegan gyros in pita bread, with vegetables, hummus, and vegan feta

Today was the informal start of our Veganuary. I went shopping for core vegan staples and a few upcoming easy meals, and we made our first vegan lunch: vegan gyros in pita bread, with oat créme fraîche, vegetables, hummus, roasted onion flakes, and vegan feta. Everyone was postively surprised – the vegan gyros was tender and flavourful, the fraîche was to everyone’s liking, and the feta was eerily much like the original.

We also discussed implementation and focus, and came to agreement: 1) major focus: sustainability and being planet friendly. No flight transports or unneccessarily long transports if local alternatives exist. 2) secondary focus: health. We might as well diversify our carbohydrates while changing things around. More beans and lentils. 3) Needs to be family compatible. The kids will sometimes get their usual fare, but will be encouraged to try alternatives.

In addition, I aim to take a generally more planet-friendly month, focused on re-use and DIY, aiming for second hand and pre-used where available.

2021 projects, #8: podcasts

Podcasts have been growing quickly in numbers during the last years, and I didn’t really clue in to that until I re-joined LinkedIn in the middle of the year for other work purposes – and suddenly, it seemed whoever I checked and followed had a podcast. Or had just started a podcast – it is apparently the Professional Thing To Do in the 2020’s.

Currently, my life mostly lacks quiet time to sit down (or go for walks) and listen to podcasts, so I have been amassing an ever-growing long list of interesting, possible podcasts to listen to; it is very low effort to follow more podcasts now that they are available on Spotify.

I used to listen to a lot of podcasts some years ago, when the kids were still small enough to need daily long walks in a stroller. It was mainly EscapePod and a few different Swedish Radio pods, and a very nice podcast with some of my favourite authors chatting about different things, the SFSqueecast, but it ended long ago.

So, my project for 2021 is: take the looong list of podcasts I currently subscribe to, and trial them to see which ones are worth keeping long term. I have one nominee for the list already, the ORION Open Science podcast.

2021 projects, #7: books

I own a lot of books. Nowadays, I mostly buy Kindle books, since the bookshelves had to go when we got twins. I now own about 700 books on Kindle, of which 400+ are read at least once. This is the result of one single Twitter account (mostly), @SFSignal, that tweets sales of SF and other fantastic fiction, under the tag sff_eBookDeal. Some of the books go for as low as $1-$2, and that’s where the majority of my digital library comes from.

I also own a lot of actual, physical SFF books. Nearly all paperbacks. We used to have a high shelf for my books along the walls of our entry hall, but when we switched apartments a few years back, that had to go. It swallowed at least 150 books, that now lying in boxes in the cellar storage.

When we started the Matmolekyler project, we started out with buying useful books. I have a bunch of those in my bookshelves (including some I got myself, or as gifts: several books by HaroldMcGee, two priced *signed* books by Gordon Shepherd). Since then, I try to buy food-science-related books when I find them at reaonable prices. That collection is now about 50 books.

I also went through a period where I was thinking a lot about food and cooking history, so I tried to find some of the earlier real cookbooks (and school household training books) from the early 1900s. There are typically cheap and abundant at used book stores, so by now I have quite a few. Including one I got at a museum, which is a copy of a 1800s cookbook along with a companion book written by a historian). And a set of two old ~1800s household encyclopedias in a new edition from a Swedish agricultural society (I had to order them special and pick them up in person). Let’s say, another 40 or so books.

For 2021, I hope to rearrange all of our (mine, really) bookshelves so that I have more SFF books accessible (since I want to re-read them anyway). I hope to inventory and index all books, and maybe even get rid of some. I need to find some good book inventory software – I have Goodreads but haven’t really used it for sorting books yet.

2021 projects, #6: scouting & leadership

The founder of Adolf Fredrik scoutkår, Ivar Åkerfelt.

My kids wanted to join the Scouts, so we put them in the queue for our local Scoutkår, Adolf Fredriks. Kids whose parents agree to help with (co)leading get boosted higher in the queue, and I do have earlier experience, so I indicated my willingness to help. And then we waited.

Not for long, it took maybe a month or so. No regular meetings were held, but we tried to meet up on Zoom each week (and if you have ever wondered why Zoom etiquette is needed, try meeting with a group of eight-year-olds and try to get them to follow a program).

There have been no outside activities yet, but that is our likely next step, so we have gone over what outdoor equipment we have and what we need. Black Friday let us buy two good sleeping bags for a good price. The kids’ great-grandmother gave them each a good outdoor backpack. I found myself hiking boots, outdoor trousers and a decent size backpack (~50 l ) on sales. Rainjackets, -trousers and boots/waterproof shoes we already have, because of Stockholm winters. We also got two pairs of skates and helmets for the kids, because one of the possible future activities is the skating ice frozen in the nearby Vasaparken, arranged every winter season by the local authorities.

So for the next year at least, I will be the co-leader of a troop of 8-year-old scouts (who will turn 9 during the year). I have so many ideas for fun stuff to do, based on my own years in the Mjölby scoutkår at home.

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.

2021 projects, #4: learn something new

I have always sought out situations where I think I could learn something interesting. 2021 will not be different. Many of the tings I have learned over the past decade are by Brownian motion and absorption – spend enough time in a community, you will pick up their interests. So I thought it would be a nice thing to learn something in a more structured fashion.

If there is one thing – something not Covid – which has popped up repeatedly in the space around me this year, it is AI and machine learning. Many papers with new neuro tools using deep learning and other ML approaches. That fantastic protein folding study. The Semantic Scholar search enginge’s new amazing TLDR:s of papers. And I attended a very interesting webinar on the possible applications of AI in music (I think it was a Stockholm AI event, but their event calendar is bugging out on me currently, so I can’t verify).

What entices me is the amazing creativity I see in many approaches – there are obviously a wide range of AI applications that I had not been able to imagine.

So I have signed up for two courses, one translated into Swedish – mostly to pick up the Swedish terms if they even exist yet, also because the translation is fantastic – and one in English from Coursera.

My 2020 project was to learn Python. Since I effectively started it in September, I haven’t come that far yet (I am at the NumPy stage), so this will be a continuing project in 2021. Also, I was gifted my friend Benjamin Auffart’s new book on ML in Python, the Artificial Intelligence in Python Cookbook, so I have resources to make this another branch of the AI learning project.