Late with this entry; wiped out by my second Pfizer shot, which I got on Friday. Glad (so very very glad!) to have it, even with the week’s worth of sleep (I might be exaggerating) needed after it.
Three new codes were added to our staged (unpublished) entries and one code was submitted by an author this past week. Twelve existing entries were edited, and as always, numerous emails were sent regarding site links that are not working. I spent time during the week on SciCodes work, as our monthly meetings were this past Thursday, and will continue with that this week in addition to putting in the final work on our NASA ADAP project.
We curate ASCL records through different activities; setting up “Today’s random code” posts is one such activity, as is following up on links that fail our link checker for some weeks. We also have an online change request form that triggers curation (though admittedly not quickly; email is a faster way to let us know about necessary fixes). But how do we know that every record gets looked at periodically? By doing a query to see which records haven’t been updated since [some date]. Each year, we look at entries from current year – 3 that haven’t been updated and examine them for possible curation. This year, that date is January 1, 2018. The query result also provides a list of linked ASCL IDs for these entries. As you can see below, we currently have 117 records that have not been updated since the beginning of 2018.
That number was a little higher a week ago. Curation work was performed on eighteen codes this week; ten of these were from the query results.
Other activity: three author-submitted codes were processed and assigned ASCL ID, and three new (unpublished) entries were staged. After we assign an ASCL ID, an editor (Kimberly DuPrie/Catherine Gosmeyer/me) writes to the corresponding author for the software to let him/her know the code’s ASCL ID and the permalink for the entry; Kim sent eight notification emails this week, along with numerous other routine correspondence by all editors. And I spent a little time writing material for SciCodes, this in collaboration with others.
This past week felt, and was, much more productive than last week. Work was actually accomplished! (I felt guilty about ignoring the ASCL Central cat, however, so he now has three new battery-operated toys, one of which he actually likes… the noisiest one, of course.)
Twenty-three new entries, some submitted by their authors (my thanks to them!), were assigned ASCL IDs and moved into production; we finished March with thirty-one new code entries. Thirty existing entries were curated; it is always a pleasure to add Preferred Citation information to an ASCL entry, and I was glad to be able to do that for a couple of these existing entries. (If the entry for your code does not list a preferred citation, please shoot me an email at email@example.com and let me know what it is; thanks!)
Social media random code entries have been scheduled through April 23; I also created and scheduled the list of March codes that will appear on this blog on Monday. It was a correspondence-y week, too, with thirty+ emails going out to code authors to let them know about a new code entry or to ask a question about a code submission or a download side 404ing, in addition to a similar number of other common every-day missives. I spent a few hours this week getting the SciCodes web domain working again; it needed several updates and new software installed. Also related to SciCodes, I reviewed slides, as second author, that first author Tom Morrell (Caltech) will be presenting later this month as part of a workshop at Neuroinformatics Assembly 2021; this consisted of reading the slides and suggesting that a comma or space be added on about three slides, as Tom’s slide deck was (as usual) excellent in every aspect.
A week of frustration and low productivity. The new laptop arrived on Monday, and though the initial move of stuff from the old machine to the new went smoothly, thanks in part to a 30-minute setup appointment that Apple offers new product owners, way more time was spent Googling for help and chatting with customer and tech support at multiple companies (either online or on the phone) than I expected. I hope to work out the remaining issues over the next few weeks, and then I expect to love all the technology again. It was not all bad, however! A new external monitor came later in the week — this to replace the old television that had been pressed into service at the beginning of the pandemic when monitors were sold out — and it is bigger, brighter, clearer, and more flexible ergonomically, than what I’d been using. Really, it’s a huge improvement! It was lovely to go to my office at UMD, though I was there for only an hour and saw only one colleague (masked and social distant, of course), the daffodils are blooming, the weather has been tee-shirt friendly, and I took some personal time, too, even though that leaves me a bit even further behind on the gigantic long to do list. This list will never be empty, of course; there are always always always things to do.
Five new codes were added to our staged (unpublished) entries and one submitted code was assigned an ASCL ID this week. Eight existing entries were edited, and numerous emails were sent requesting information from code authors and others about new entries, site links that are not working, and an edit resulting in a new bibcode for one entry. I did not get any SciCodes work done this week, so that is something for me to work on this week in addition to the usual work on the ASCL. I’ll be concentrating on moving new entries into production at the beginning of the week, however, as that is my top priority.
For spring break, or even not for spring break, this was a busy week. I gave a Physics Colloquium, Schrödinger’s code: Opening the computational box, at Michigan Tech on Thursday; links to the slides, resources/sources, etc. are available online. It was a new talk, and though I could repurpose some slides from various other talks, creating new slides and working out the flow took a good bit of time. The colloquium was scheduled between two meetings of the SciCodes consortium. More about SciCodes is below.
Three code entries from our backlog were edited, assigned ASCL IDs, and moved in production, and three new codes were added to our staged (unpublished) entries. We have hundreds of entries staged; some of these don’t yet meet our criteria and may never do so. Thirty-one entries were curated and social media random code entries have been scheduled through March 31. One would think that scheduling these random code entries would be quick, but it took over three hours to stage the eleven needed to finish out the month, as entry curation is part of this work.
The SciCodes consortium holds two meetings on the same day to accommodate different time zones; members can attend either an early or late meeting. After the early meeting, a couple of people stayed in the Zoom so we could talk, as several people new to the group had questions. The meeting made clear that I had not prepared any on-boarding assistance, so that will have to be corrected.
This coming week, I will send out meeting minutes for the SciCodes meeting, try to figure out what I need to do to get the SciCodes web domain working again, meet virtually with a colleague (I hope) about our NASA project, and spend some number of hours getting a new machine set up, as it is supposed to arrive early in the week. I’m sure I’ll be thrilled with it once it’s set up, right? I’ll also be going back to my office at UMD part of one day this week; it’ll be only the second time I’ll have been in it since before last year’s spring break.
On Thursday, March 18, I am giving the physics colloquium at Michigan Technological University (MTU), which has hosted the Astrophysics Source Code Library since the ASCL’s inception in 1999. Despite having worked on the ASCL for nearly eleven years, I’ve never been to MTU; though I wish the visit could be in person, the talk will be presented virtually over Zoom. The presentation abstract is below, as is a link to the slides and links for all of the citations and resources mentioned in the talk.
Abstract: Though computational methods are widely used in many disciplines, many researchers do not share the source code they develop, making it difficult to replicate and reuse the work. This presentation will cover the changing landscape that includes funders’ requirements, policy changes for existing journals, community resources, and more, that make it easy to release and archive codes to ensure they are available to support the research they enabled, improve the reproducibility of science, increase confidence in research, and meet new requirements made by funders and journals in many disciplines. It will also cover how the Astrophysics Source Code Library (ASCL), which has been working since 1999 to improve the transparency of research by registering open codes used in research, has made it possible for software to be cited as a first-order research object, and how researchers can garner credit for their codes by having them cited correctly and improve papers by including citations for the computational methods that enabled the research.
Astronomy and Computing (A&C)
Computational Astrophysics and Cosmology (ComAC)
Computing and Software for Big Science
Computer Physics Communications (CPC)
Journal of Open Research Software (JORS)
Journal of Open Source Software (JOSS)
Change leaders and guidelines
CITATION file format (CFF)
FORCE11/FORCE11 Software Citation Principles
Software Sustainability Institute
Working toward Sustainable Software for Science: Practice and Experiences (WSSSPE)
Social coding sites and archival services
DOE CODE; more information
arXiv/arXiv Next Generation
Software licensing resources | Licensing Astrophysics Codes special session at AAS 225
Papers with Code
Cited sources (in order of appearance)
Ince, Hatton, & Graham-Cumming (2012)
Allen, Teuben, & Ryan (2018)
Ryan, Allen, & Teuben (2019); Data and code
Collberg, Proebsting, & Warren (2014), PDF
Howison & Bullard (2016)
Mangul et al (2018)
Zorotovic, Schreiber, & Parsons (2014)
Neupane et al (2019); Vice article
DOE policy FAQ
NASA ROSES policy
Nature Portfolio policy
AAS Journals policy
This past week, I refined the abstract for a talk I’m giving this coming week at MTU; I also did research into funders’ policies on code release to ensure my knowledge about them is up-to-date, this also for the upcoming presentation.
Four code entries submitted by authors were edited, assigned ASCL IDs, and moved back in production, and fifteen entries were curated. Several entries have had two bibcodes, a result of changes in authorship/author order. If you’ve ever noticed when looking at our dashboard that sometimes, ADS has >100% of ASCL codes, these extra bibcodes are why. I finally devoted time into tracking those down and sending the information on the duplicates to ADS to bring us back into agreement. This is a low-level issue, but it’s nice to get this loose end resolved.
The ASCL and similar efforts in other disciplines have come together to share ideas and work cooperatively in areas of mutual concern; at the moment, the coalition is called SciCodes. My main activities on SciCodes this past week has been getting the next 12 months of meetings scheduled, the schedule sent out, and confirming a presentation for it.
Peripheral to the ASCL, though also mostly because of it, I spent a ridiculous amount of time one day looking at new Macs. The OS on my current MacBook Pro is now too old to allow me log into UMD, which means I cannot access journals through the UMD Libraries on this machine, a critical need for ASCL work. It’s also having some issues, one of which, running hot during Zoom meetings, I have been working around by putting the machine on a bag of frozen mixed veggies. I don’t like upgrading and do it only when I absolutely have to. Do I want two ports or four? Apple’s M1 processor or Intel’s i5 or i7? How much memory, how much storage? And why don’t new MacBooks have SD slots?? A new machine is on its way to me.
This coming week will include the presentation at MTU, work on our NASA project, and the SciCodes meeting.
This past week has been pretty busy, with a presentation at SIAM’s CSE21 meeting on Wednesday and attendance at other software-related sessions. Eight new code entries were moved into production, three new entries staged, and code authors submitted seven new entries that will be worked on in the coming week.
Social media random code entries have been scheduled through March 17, and the forum and blog updated with February’s code entries. Curation and/or archival work was performed on or for 15 holdings; this included updating some entries with preferred citation information, updating links, and adding keywords, and downloading new versions of software that had been updated since we last downloaded it. Correspondence was sent to at least 24 authors.
In addition to working on newly-submitted codes, this coming week will include work on a presentation that will be given later this month, and progress on our NASA project continues.