FLOSS Weekly Episode 733 Transcript
Please be advised this transcript is AI-generated and may not be word for word. Time codes refer to the approximate times in the ad-supported version of the show.
Doc Searls (00:00:00):
This is PHAs Weekly. I'm Doc Searles. This week Dan Lynch and I talk with Tim Bonk of Open Source Science about that topic and about the ven overlap that needs to be increased between open source software and hardware and code writing on one hand and open source science development on the other. These are more separate than they ought to be, and he's leading the effort to move those things together. Lots and lots of interesting topics. And that is coming up Next.
This is TWiT (00:00:31):
Podcasts you love from people you trust.
Doc Searls (00:00:40):
This is Floss Weekly, episode 733, recorded Wednesday, May 24th, 2023, open Source Science. This episode of Floss Weekly is brought to you by Collide. That's collide with a k Collide is a device trust solution that ensures that if a device isn't secure, it can't access your apps, it's zero trust for Okta. Visit collide.com/floss and book a demo today. And by bit Warden, get the password manager that offers a robust and cost effective solution that drastically increases your chances of staying safe online. Get started with a free trial of a teams or enterprise plan, or get started for free across all devices as an individual user at bit warden.com/quit. Good morning, good evening, or good whenever it is. Wherever you are. I am Doc Surles, and today I am joined. This is last weekly. I had to say that and I forgot, but not really, cuz I just remembered it. Anyway, I am joined today by Dan Lynch and it's early today, <laugh> for us. So
Dan Lynch (00:01:52):
It is. Yeah. Hey, doc, you're okay?
Doc Searls (00:01:54):
Yeah, I'm great. I'm great. Seven early, early rise here on the West Coast. But you're, you're, it's evening already for you there, so
Dan Lynch (00:02:02):
How you doing? Eh, not quite. It's afternoon, mid-afternoon. Oh, that's right. I have less excuse than you to be sleepy at the moment, <laugh>. So I'm gonna blame my allergies. I think it's the there's a lot of pollen around at the moment. That's kinda,
Doc Searls (00:02:13):
I I, I, I blame mine too, because but I'm always allergic to California. It's mm-hmm. <Affirmative>. There's something about it, even though I live here and vote here. But, you know, it happens. So, what's that T-shirt? I'm, I'm seeing half a cartoon on your T-shirt.
Dan Lynch (00:02:29):
Oh, this is, do you guys have the Mr Man in America? Roger Hargraves. It's a kids' characters thing. This is Mr. Bomb, he's called, he's covered in bandages because he is always having accidents. That's why he's called Mr.
Doc Searls (00:02:41):
<Laugh>. No, no, I don't. But I've, I haven't watched cartoons since or looked at cartoons since I was a kid. Mm-Hmm. <affirmative>, which is more than a <laugh> the better part of the century ago. So, are you familiar with our guest today in open source science?
Dan Lynch (00:02:59):
A little bit. Yeah. I've, I have done some I did a bit of research this afternoon. I did have the advantage of not being crazy o in the morning like you, which is good. <Laugh>. So I, I had a little read around on osi, which we're gonna talk about, and some of the projects and stuff that, that they've been involved in. It's a really exciting area, actually. I think there's a massive crossover between the science world and, and the open source world.
Doc Searls (00:03:22):
So I'm gonna hurry up and bring him in because we're off to a late start. Guest is Tim Bonk. He's the community lead for open source science O S S C I, a new Nu Focus initiative in partnership with I B M. It's aim is to accelerate scientific research and discovery through better open source in science. And there's a lot more to his bio, but it's all these questions we can ask. Welcome to the show, Tim.
Tim Bonnemann (00:03:49):
Hey, good morning. Good morning. Good afternoon.
Doc Searls (00:03:52):
Yeah. So where are you? What, what part of the day is it for you?
Tim Bonnemann (00:03:56):
I'm on Pacific Time. I'm based in San Jose, California. Oh,
Doc Searls (00:03:59):
Cool, cool. Well, not that just a, a four hour drive for me at this, this point. I'm in Santa Barbara, so, so so tell us a, fill us in on what opensource science is about what NUM focus is about as well, and is it pronounced that way?
Tim Bonnemann (00:04:15):
Yeah, it's num focus. Okay. Yeah. So num Focus is a nonprofit. And surprisingly few people know about it. It is home to a lot of the most popular Python projects, num, PAI SciPi, Jupiter Panda, psyche Learn, et cetera. They have dozens of sponsored projects and all. I think also several dozen associated projects that are onboarding. They're in Austin, Texas, and they're small, relatively, I think they have like 10 or so employees, several million annual budget. So very small compared to, say Linux Foundation or others in this space. An open source science was launched last year at the, at the SciPi conference in Austin. The idea came out of I b M research, but it was intentionally set up a neutral ground as a community initiative under non focused a lot of the Python projects are very relevant, relevant to the mission of open source science. So it was a good home. And yeah, it's about open source science. It's about accelerating scientific research and discovery by improving any and all aspects of open source and science from, you know, onboarding students and young scientists all the way to, you know, more institutional changes that might encourage better practices in science when it comes to open source,
Doc Searls (00:05:47):
It seems to me, because and I'm wondering, this is, I'm gonna project something here, which is that I'm having been around open source before we called it that, and it was still free software back in the eighties and nineties. The, the default within code writing in general was it was all owned. It was all closed, it would all belonged to companies. And in a similar way, I think science has been in a similar place. It always looking to create patents, to create walls, to lock things up to hold them in a proprietary way. Is, is open source science behind open source code writing and publishing in that sense? Or is, am I just guessing at that?
Tim Bonnemann (00:06:32):
You mean in terms of development? Yeah, or in terms of
Doc Searls (00:06:34):
And and what
Tim Bonnemann (00:06:35):
Doc Searls (00:06:36):
Yeah. And, and, and the mentality about it as well. Like if I, you know, I'm, let's say, I mean, I realize most people doing science are doing it either inside the academy of one in one way or another, or for a company. And those two institutions have different reasons for wanting to hold things themselves, right? Yes. I mean, when I, when I started as a fellow at uc, Santa Barbara, I had to sign something saying every thought, every invention I had while I was there belonged to them. And but when I did the same thing at Harvard, they did nothing of this sort, but more or less communicated, we just hope you remember us. When you succeed at something, it's a different mentality. But in both cases, the assumption was that the intellectual property, whatever it was belonged to the institution, not to the individual. And the individual was less free to share this stuff. Right. So I'm just wondering what, what, what the institutional flywheel are and, you know, and how those compare.
Tim Bonnemann (00:07:37):
Yeah. I think in academia I mean, people publish research and along with that research, they, they publish artifacts, right? They publish or they may publish artifacts, let's say. I think there has been an increasing trend towards, towards open science in, in, in among some in academia, let's say. And so they publish research and along with that they might publish data sets or models or open source software that they've written for the purpose of completing the, the research. And those are the people we're trying to, to reach, right? And we're also want to try to encourage more people to, to follow those, those practices. In the, in the private sector, yes, there is a lot of proprietary research. However, there's also with all open source, there are areas where, you know, the rising tide lifts all boat type of approach where you have tools that make sense to be shared across competitors, even so, and, and those we are also trying to, to reach. So I'd say it's I mean it's not completely you know, a hundred percent open source all the time, but there are enough people that are very committed to open source in science and are championing open source across the, the whole life cycle of, of research.
Dan Lynch (00:09:12):
That's that's really interesting Tim, cuz that docs kind of got the opposite thoughts on it to what I had, which was, and to be fair, docs got a lot more experience in academia than I do. I went to a university or college, as you might call 'em, in America, but I did a degree, I didn't like do teaching or anything. But I always thought a large part of scientific community. Anyway, a lot of it's to do with peer review is a big thing. They talk about peer review. You've gotta be able to see and replicate what the other people are doing. So I would've thought that mindset would fit in really well with open source in a way.
Tim Bonnemann (00:09:44):
Yes. Yes. And the people we've been connecting with so far, we're still new, right? We're less than a year old. Mm-Hmm. <affirmative>, the people we are connecting with initially are, are very invested in open source and are leaders in their respective fields in open source. And in fact when you mentioned reproducibility, we're actually in the process of launching a new interest group on reproducible science in June which will address these challenges, right? When you have research that relies on software and data and models, you know, if it's, it's, it may be very hard to keep it reproducible over time if you don't maintain it, if you don't tend to it. And so we're gonna bring people together to work on possible approaches to, you know, come up with better options for keeping science reproducible.
Dan Lynch (00:10:35):
Mm-Hmm. <affirmative>. Yeah. makes a a lot of sense to me. But as I said, I, I'm no expert in that field, but in that area, I suppose, of academia it seems as a, there's a kind of, to me it feels like there's a, a, a close link in the kind of technology as well because I, I think about things like scientific Linux, which was it was kind of spun out of Red Hat, I believe originally, or, or fedora or one of those projects which became a really popular thing. I remember reading, I don't know if this is still true, but I'm gonna go back now, it's anecdotal evidence, but something like 18 of the 20 fastest craze or supercomputers in the world. Were running Linux at the time, or Lennox Kernel, which we always championed obviously as Lennox people, even like, hey, we run the stuff that does the heavy research. Is there a big crossover there with the technology suppliers as well? Cuz you've got, like, obviously a lot of the universities are doing, are getting in pro stuff like Red Hat contracts. You've obviously got IBM Red Hat, obviously together now and so on. Is there a cost over there as well?
Tim Bonnemann (00:11:38):
I believe so. I mean, we haven't we haven't looked at, well, I'm, I'm pretty sure there is anecdotally we haven't looked at these like advanced computing facilities and what they're using. But the, the groups that we have, which initially is chemistry and life sciences and climate there are, in their work as practitioners, they're using open source up and down,
Dan Lynch (00:12:12):
So mm-hmm. <Affirmative>. Yeah. It makes a lot, it makes a lot of sense to me. I, I know a lot of things come out of, you know, lakes of Nasser and stuff like that. They use a lot of this kind of stuff. They're ran into Python, I believe, at Nasser. I was told that once. I don't know if that's really true. I assume they are. It's interesting that you mentioned non focus. I'd never heard of them either. You, you said not many people have heard of 'em, but of course I know Num Pi and I know Jupiter. I've used Jupyter Notebook a lot, but I never heard of Num. Yeah, they're
Tim Bonnemann (00:12:37):
Also, they're also the they're also behind the very excellent pie data mm-hmm. <Affirmative> Meetup network and Pie Data conferences. I just went to, had a chance to go to Seattle for the Pie Data Seattle Conference, and it's a, it's a great community. I was very impressed. It's a great conference, great content great vibe. And yeah. And they are kind of in the background surprisingly. But then when you ask people like, do you know, you know pandas? Do you know Jupyter? Yeah, of course. So mm-hmm. <Affirmative>.
Dan Lynch (00:13:11):
Yeah. It's interesting. Maybe they just don't promote themselves as much. Maybe they're, maybe they
Tim Bonnemann (00:13:15):
Dan Lynch (00:13:16):
In the background. Maybe they're happy to be, you know, in the background promoting these great projects. Yeah. it's very, very cool. Yeah. no, it seems to me that like what you're trying to do is, is bring, obviously you're trying to bring people together across the science community, development community, open source community. What kind of tools and things do you use to do that? You've, you mentioned interest groups. What kind of stuff do you, do? You do?
Tim Bonnemann (00:13:37):
Yeah, so our approach is, is is in a way twofold at the moment. So we we're starting out with five interest groups three verticals, which are, you know, chemistry, material science and life science, healthcare and climate sustainability. And then we have two groups that cover horizontal themes. One on reproducibility, which is launching in June. And the other is about creating a map of science, which is gonna be a tool to discover and explore tools, open source tools in research, and the related scientific published papers and the people behind both. So we're bringing together, we have a few dozen people, but growing mm-hmm. <Affirmative> we're bringing together you know, experts, scientists who already are heavily invested in open source, who have successfully pled open source in their, in their field and other stakeholders, some foundations, government, some private industry, and get them together or build community, get them to exchange you know, talk about what they're working on, how they're using open source what roadblocks, what challenges they run into, what pain points they experience.
And then from there, look at how things could be improved. Basically, that's, that's kind of the the idea, but it's really a an opportunity, a venue for people to connect with each other and learn from each other and share notes. That's, that's basically, and we, we suspect that some good will come out of that, right? Mm-Hmm. <affirmative>, and these are gonna be, there's like an official charter, so very soon they're gonna have co-chairs and it's gonna be a bit more, you know, official and organized. But it's been, it's been fun getting these people together. And then the second approach is more a, a wider lens of building a, a wider community for people interested in open source and science, who may not necessarily want to commit to a working in a, or collaborating in a, in a working group. And so we had a first meetup in February at uc, Santa Cruz. We are gonna have lots of meetups this summer and fall. We're just lining them up and finalizing details and Chicago and Austin, and a bunch of places in Europe. And so that's where we're going to try to get people, make people aware that this new initiative exists, and get them excited about the opportunities we want to connect as part of this initiative, connect scientists with open source developers and, and facilitate that exchange for, you know,
Who knows upskilling scientists or creating opportunities for open source developers to contribute to projects that are, that have a science focus. So those are kind of the two prongs. And then in the background, I'd say we just went to open source Summit in Vancouver. Mm-Hmm. <affirmative>. And we've been very busy trying to connect with the wider ecosystem. There's lots of organizations and communities and, and individuals who already have been working on related efforts there, where there is some overlap or some kind of relation, and we're just trying to, you know, plug into all the right spots and, and find synergy there.
Dan Lynch (00:17:09):
Hmm. Yeah. That that makes sense. And I have to ask the kind of I dunno how I'd put it, it, it's not exactly a dirty question, but you mentioned about funders and stuff, I noticed a lot in the documents and some of the, the pub the publicity stuff. So I'm assuming it would be hopefully a way for projects and companies who need these projects to say, we need, you know, X feature or, or this to work better, or whatever it is, we'll pay you x amount to do it. Is there a link there possibly as well?
Tim Bonnemann (00:17:38):
Yeah. So we don't have anything concrete <laugh> lined up yet in terms of Yeah. Like concrete project, but yes. So a big issue that has come up at pretty much all the, the, the meetings we've held and all the conversations we've had is, you know, funding and, and sustainability for open source. And so there are lots of, you know, challenges and some challenges are maybe even the worse and in the private sector. And so yes, we want to find ways to address that. And we're gonna talk about, in fact, there is a, there's probably gonna be an interest group on just funding and sustainability that will form, we have a, we have kinda an intake form and, you know, people have been signing up to join the work and they can suggest topics of their own right in addition to the five that we're starting out with. And so funding and sustainability is, is a very, one of the most commonly mentioned topics. So yes there should be better ways to ensure the right projects are, are, are funded and sustained as needed.
Doc Searls (00:18:54):
So I have some questions lined up here sure. To leverage off some of what we've already talked about. But first, I have to let everybody know that this episode of Floss Weekly is brought to you by Collide. Let's collide with a K Collide is a device trust solution that ensures unsecured devices can't access your apps. Collide has a big news. If you're an Okta user, collide can get your entire fleet up to 100%. Compliance Collide patches, one of the major holes in zero trust architecture, device compliance. Think about it, your identity provider only lets known devices log in to apps. But just because the device is known doesn't mean it's in a secure state. In fact, plenty of the devices in your fleet probably shouldn't be trusted. Maybe they're running on and out of days OS version, or maybe they've got unencrypted credentials lying around.
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Tim Bonnemann (00:21:31):
Yeah, 50 in our Slack. Also, you, you mentioned infrastructure earlier, so we have a Slack for the people that are working in the interest group. So that's about 50, including the non focused team and including the two of us at I B M research that run this on the IBM M side. We have a little over a hundred on our newsletter. We have I think I wanna say 40, 50 lined up right now to join the interest group. So we're starting to you know, weave them in. We just added, like on Monday, we added three new ones to the map of science interest group. And we're gonna start letting people in over the next weeks, few weeks and months, basically. The idea once we're a little bit more organized, and once the groups have a bit of a initial agenda figured out, like a, like a work plan it's, the idea is for it to be open, right? So anyone can basically, you know, attend or listen in, or if they want to contribute, they can, they're welcome to contribute. So it's, it's supposed to be open. We're gonna share everything basically notes you know maybe even recordings on, on our site. So it's it's supposed to be in the open. It's an open source, you know, community initiative. Just need a little bit more time to, you know, get these groups, give them enough structure so they can have a good, good start out of the gate.
Dan Lynch (00:23:07):
Mm-Hmm. <affirmative>. Now Tim, I noticed that you sent us some, hopefully sent us some stuff some topics to mention. And you touched on it there, the, there's the Amsterdam Declaration of Funding research software Sustainability, which is being kind of collaborated on at the moment. Yeah. can you tell us a bit about that? And also, I noticed that it finishes 25th of May, which is tomorrow. So if people wanna reply, they'd better like, stop. Well, you can keep listening to this or watching it again on it now.
Tim Bonnemann (00:23:33):
Yes. Yes. So you go, can go to our medium. It's open source science. Oh, it's, it's right on the screen there. Yeah, so Amster Declaration is a, is a, is a, is a conversation that we're involved with, involved in where some of the major funders of research are coming together to figure out how ca how they can can yield better open source results through the, the way they fund projects, right? So mm-hmm. <Affirmative> example, you know, I'm a funder and you know, I give you 800 million for cancer research. And then maybe, oh, by the way, you know, all the software that comes out of that grant shouldn't just be open source on paper, you know, has the, in some GitHub and be open source, you know, in theory, no, it should live in a, it should be part of an existing project.
It should have a community. There should be you know, you should take good care to make sure it lives beyond the, the duration of the grant, right? It can, it can contribute to the whole ecosystem. Anyway, those are kind of the, the strings you might want to attach going forward so that someone who applies for these grants from the get-go has to think about, okay, so how I'm gonna implement, you know, good practices, maybe I need a community manager. Maybe I need someone who has open source experience and can connect these efforts from the project back into the, and weave them back into the ecosystem, right? So that less of the work that gets done in these projects is wasted by being abandoned once the, the, the grand has ended, or the, the research paper has written has been written, or there are many areas in, in, in science where that happens. Right. But by the way, the, the deadline, I guess, is for just this current draft. I think it's an early draft. That's right. Version 0.03. I think it, I think it might get, I don't know exactly what the timeline is, but it might take until next year until they sign it.
Dan Lynch (00:25:46):
Mm-Hmm. <affirmative>. Yeah, I should have said that. It's for the current draft. Yeah. It's not like all over Dawn <laugh>, you know, finished tomorrow. I'm sure there's much more to do on that. We actually have a question from our chat room which is interesting. I suppose it kind of relates a little bit. We'll see how it goes. This is web 7 0 12 is the user who says can you please explain why open source that's in speech quotes always gets co-opted owned and monetized. It says the best things in life are free, so we must support them with every dollar we can. Interesting. <laugh>, I don't know, have you got any thoughts on that?
Tim Bonnemann (00:26:22):
Well, I, I mean, I can't speak for all of science. I mean, the, the people that we're talking to are passionate about advancing whatever field they're in, right? They're, they're, they're discovering things. They're advancing science, and they are they're eager to, you know, ha not only have the best tools available for them, but also to contribute back and, and make sure these tools have a, you know, have a good place to live. And mm-hmm. <Affirmative>. So I'm not sure if they're into co-opting or monetizing <laugh>. No, no worries. It's a good answer. It's a difficult question. I, I appreciate that.
Doc Searls (00:27:03):
I, I, I have some thoughts about that because Uhhuh <affirmative>, you know, have you followed it for a long time, but I think most, it doesn't necessarily get co-oped or monetized. I think I mean, you want open source to be useful and used. It's going to be used by business inevitably. And many years ago when I was working in the UK with BT and JP Rago, Swami was the chief scientist there, we were talking about this and came up with what we call, because effects, meaning you make money because of open source. You don't make money with it, you know, you don't sell it. But it's laying around and you use it. I mean we had Tim I mean Greg Crow Hartman on last week, one of the alpha maintainers of Linux. And you know, the, you know, he, you know, he works for a company, you know, he works Celtics Foundation now, but he worked for other companies before that. In fact, it was Dan Fry at at I B M when I talked with him. He said it, even though IBM has been very, was at the beginning, very supportive o of open sources and idea it took him five years before they realized that all the kernel developers, the Linux kernel developers are completely independent <laugh>. And I suspect you're in a similar position there, Tim, as an independent operator, you know, working for I B M and, and helping with this, with this project.
Tim Bonnemann (00:28:31):
Yeah, I mean, the, the, I think the reason I b m research is interested in this is they realize that there is a lot of science left to be done, right? We're facing some very, you know, existential challenges as a planet, as a humanity, as a species, and we're gonna need a lot of science over the next few years and decades to, to address some of these things. And without a strong open source motor, it's just gonna take that much longer, and it's gonna be that much more expensive, right? So that's kind of, I think the, the, the, the interest on, on the one end. On the other, it's also creating opportunities for some of these excellent scientists to connect with the community, which is a you know, it's a, it's a good thing to go out there and and, and be part of these conversations, be part of these you know movements in specific fields to, to tackle certain challenges together. And so we're with this initiative at NUM Focus, which, by the way, num Focus is also staffing up. They're hiring a program manager. So it's gonna be more parody soon. But we're creating a venue where not only IBMers, but also other people from other companies or organizations or foundations can, can, can benefit from that kind of community exchange.
Doc Searls (00:30:09):
Tim Bonnemann (00:30:10):
If that answers your question, <laugh> No,
Doc Searls (00:30:12):
It does. I, I we're also passing notes in the background and so forth. I actually have a, a question that may seem a little off the wall. So I'm, but you mentioned standards earlier, and you have these interest groups and I am so not built for, I, I don't have a bladder big enough to deal with <laugh>. The, the, the wait times there are in developing developing a standard. I'm working on one for like the last four years with the I e e. And, but I'm wondering if there's, if there's some overlap with, with standards working groups or working or leveraging your interest groups over to working groups, which I, I really, they differ with ISO and with I E E E and with, with I E T F. They all have different, different approaches. But it's a lot of, a lot of sitting around and a lot of arguing and a lot of filibustering by people who have vested interests or personalities and other things like that. Very different than you have a bug, I submit a patch <laugh>, you know, it goes through modern, it goes, there's a, there's maintain our main committers maintainers, there's, there're standard kind of simple standard ways that open source code gets, gets approved. Every code base is a little different as different personalities in it, but it's well understood how this stuff works. But standards bodies, man, that's, that's, that's a very different animal, but you need them. So Yeah. How do you, how do you do that?
Tim Bonnemann (00:31:43):
Yeah, I think at this point we were much more interested in the latter in the, in, in stuff getting done. And if people, if we can make connections, if we can get people to coalesce around, let's say a specific you know open source project in let's say, or related to material science, and we can get people to collaborate and, and, and push this particular project forward, I think that's, that's what will make us happy. Right? We haven't really talked about standards that much. Yeah, I'm sure it'll come up at some point. And then there might be other you know organizations that might want to take over. Are we gonna be at a I e E conference in, in Chicago in July so I can
Doc Searls (00:32:27):
Oh yeah. Look great. Maybe I can,
Tim Bonnemann (00:32:29):
I can find out more
Doc Searls (00:32:30):
<Laugh> Well, this, this is the IRI I'm working with on, on this one. But here's, here's what I feel like we're missing a little bit with some of the i e e ones that I'm, I know about, and it's not, and I, there's not any criticism on the i e e at all. It, it's really about the way standards are cooked, right? Where you're not trying to specify tech, you're trying to specify a framework or a methodology where lots and lots of different, say protocols or code bases could be involved, but you have to attract developers. That's the thing. And one of the arguments I've heard a lot is, that sounds great, but that's a 50 page thing. I don't even wanna look at it. How do I adopt this? And having the voice of a developer in the working group saying, I can use that, or I can't use that, or that's not gonna, that's a very good bait to put out for developers. If you want the standard to actually be adopted would be really helpful. <Laugh>. So I have, I'm projecting a fantasy here, but I'm, but I'm wondering whether or not, you know, what you're doing could help facilitate some of that cross fertilization? Yeah, I think,
Tim Bonnemann (00:33:40):
I think I think we're probably like a couple steps earlier in the, in the kind of on the mature <laugh> on the maturity ladder <laugh>. But for example, the this very exciting group that we have on, on, on building this map of open source science is about, so imagine some kind of interface or a web app or something where you can just, as a scientist type in your, your area of interest. It'll give you the the long tail of open source tools that are likely related to your query. It'll also show you the related published research and the people behind both. So you should have an instant kind of lay of the land of maybe a hidden network of people and artifacts and, you know, tools and research that you might connect with. So that should be useful in it by itself.
We hope that it might encourage people to you know, join existing efforts versus reinventing the wheel so it could, so it's not quite a standard yet, but if you can get people to coalesce around you know existing stuff that they can agree on as useful versus just having 20 or 40, 60 different tools that basically this, you know, very similar thing. So that could be one step in that, in that direction. So so that's part of the, we're starting to I actually just this week I'm starting a little kind of mini survey just among a tiny group of people in, at the company I work at to see what open source tools they have been using this past year in their work. And so that's kind of the mini kind of first very, very unscientific just to kind of get a initial snapshot of, of some team somewhere and then apply that over time to more broader audiences and see what they're using and see how they overlap or what tools they may see that they haven't heard about that they thought, well, this is really, this is great, right?
So I mean, finding tools and then knowing what tools are healthy, what tools are you know, active, are being actively maintained, have a good community behind them. All those things I think could lead over time to, you know, people coalescing around the strongest projects, but also then down the road, maybe standards. I don't know, we'll see.
Dan Lynch (00:36:19):
Excellent. It, it's a, it is really it's one of those things that we see so much in the, in the open source community, and I'm sure it happens in science as well, but people o you know, overlapping. So rather than finding a tool or a project that might already be working on what they're working on in their area we get the reinvention of the wheel that you talked about, that kind of thing of like, oh, I'll make my own one. It'd be really great to kind of get them together around those sorts of things. In the information you sent us, you mentioned about some of the overlap you've got with things that some projects like the next foundation have done, like OS climate, which I have to confess, I dunno much about. Can you tell us anything about that area or, or any of the, the, what's going on over Don't tell not about OS climate? I know you are working on that specifically, but what's the kind of crossover there?
Tim Bonnemann (00:37:05):
Yeah, so and by the way, that's the only I think person I wanted to meet in Vancouver. I didn't get to meet, so we have to follow up some other time. Oh, right. But there are, so Linux Foundation is of course, huge and they've been around for a long time, and there are definitely a bunch of you know projects and or even foundations or people that are very relevant to what we're trying to do, right? So we're, we're trying to connect with them all. They have this new, I think relatively new I dunno if it's a, that's a project, I think it's a project. I'm not that firm yet about the nomenclature of Linux Foundation ecosystem mm-hmm. <Affirmative>, but os climate deals with open source, that's, that addresses climate change or battling climate change. And so, you know, we have an interest group that's starting on climate and sustainability.
So the assumption is there's likely gonna be some overlap either, you know, people or topics or work products. So we don't want to re reinvent the wheel either, so if there are existing efforts that we can connect with, that we can plug into, that's, we definitely wanna find out what we can do there. Right. the other I mentioned, I think it's another oh yeah. So like for example, there's I dunno if you've heard of chaos. Hmm. It's it's about measuring open source project kind of performance and health over time very relevant to us at some point, right? As we build out this map to, to kind of enhance our view of the land with these data points, right? To see, you know, for example if you're a funder of science and specifically of science or research software, wouldn't it be great to see what are the dependencies and what are the projects that need support right now versus next year, right?
What are the critical dependencies? And so, so data points that might come from, from initiatives like that could be super helpful for what we're trying to accomplish. So yeah, so there's, and there's plenty more out there. There is we were put in touch on a, with a project that deals with I think, battery technology and, and battery, I think both hardware and software. And so that might be related to our material science interest group, right? So anyway, yeah. So we're like, we're super busy trying to weave our way into all the right corners of what's already out there.
Dan Lynch (00:39:53):
Mm-Hmm. <affirmative>. Yeah. that makes sense. It, it is it's really cool to see all these kind of groups coming together. I was interested in, there's lots of open source interest groups interest groups, not the, the right term. Again, nomenclature, whatever, don't, please don't hold me to that. But I was thinking about, there's lots of foundations obviously out there in the open source world, you, you of around development. You've got things like suffering, like interest cyber free and conservancy. Please don't get angry about me if I forget to mention another one. I'm thinking to people listening. Have you got any, have you approached any of those kind of people or are you looking at trying to get some of those bodies involved maybe as well, because they might know projects that could be related or could help each other, or, you know, help?
Tim Bonnemann (00:40:36):
Yeah. yes. We there's there are foundations out there. So for example the, I can't confirm any <laugh>
Dan Lynch (00:40:53):
Tim Bonnemann (00:40:53):
Mm-Hmm. <Affirmative> any concrete agreements yet mm-hmm. <Affirmative> but I just wanna mention, there is a, a foundation out there the Sloan Foundation and one of their programs is about creating open source program offices or OPOs at universities, right? So they, I think they had a, an initial pilot with six universities, including uc, Santa Cruz and I think they're about to launch another six, I think. And so this is the idea of giving open source a more strategic home at a university, right? So have a central, you you're familiar with the open source program office, I'm assuming so mm-hmm. <Affirmative>, it's basically a central hub that can, you know, coordinate and, and drive and measure and advance open source across the entire organization versus each department doing their own thing, right? So we've been working very closely with the OS at us, uc, Santa Cruz, and we are very interested in, I guess, kind of piggybacking on these efforts as we can, you know, with an osbo it's much easier for us to get a view of the, you know, open source science that's happening at a university, right?
So there are foundations like that, that both kind of have an interest on and are working on projects that advance open source at an institutional level in the academic sector. But they also fund other projects including for example gen Zuckerberg Foundation funds individual projects as well. So there is, so we're, yes, we are connecting with organizations like that.
Doc Searls (00:42:43):
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Tim Bonnemann (00:46:14):
There? So you can't see it yet. We, we are getting ready to well pull in a few more resources and then hopefully start prototyping soon. We definitely want to get something on the, on the web before the end of the year. It's about a, so one of the challenges apparently is that many of these open source efforts are a bit disjointed, right? There's a lot of silo going on, people working in their little corner of science not even talking to colleagues at a different department or a different company. And it is also hard to track which open source projects have been driving certain types of published research. Jan Zuckerberg Foundation did an awesome project last year where they really analyzed a, a huge pile of medical research and tried to pull out the references to open source projects and normalized them.
Cuz everybody, there's no standard talk about standards. People, you know, link to them. They, they quote them, they have 'em in the footnotes it's all over the place and they reference different versions, different parts of a GitHub repo. It's like, it's a mess, right? So these this team at CZI applied some, you know magic to, to kind of clean up those references and normalize them and then to do, do some analysis on them. And I can, I can send you the, the link to the medium post after. It's really fascinating. So that's another challenge, right? So it's, it's kind of hard to, you can, you can probably find it, but it'll take you forever to to find those linkages, right? And so what does idea of map of science is about is to, to connect those dots, right?
So on the one hand you have open source projects that are related to science. On the other, you have published research that has referenced any of these open source projects. And then behind both you have people, right? So, you know, maintainers, contributors of these open source projects as well as authors of the research. And in some cases they overlap, right? So, and there's other things you could also plug in, like data sets or, you know, models or funding events and things like that. But for just to get started, you have open source projects, papers, and people. And so this tool will allow you to search for any given topic and it'll show you a, a small map that connects these dots, right? And hopefully you'll find some people you should probably talk to if you're, if you're, if you're going, if you're starting a new research project, there should be people that and, and communities behind them that are relevant to what you're trying to do.
You might find some research you hadn't seen before. So that's kind of the, the idea. And the hope is that it'll make it more likely for people to build on what's already out there and connect with the, the people already involved in that particular sphere they're entering. And then there's other things that could be done once that's, once that initial kind of, those initial use cases have been addressed. I think there's other there's other use cases for funders, for institutions like university that could make this super interesting for them to you know, to to see a map of their particular part of the universe.
Doc Searls (00:50:08):
A a couple of points about that one is, I remember because I was a p philosophy major a terrible one, but I was one that it said that philosophers know more and more about less and less, about more and more until they know nothing about everything. Well, scientists know more and more about less and less until they, everything about nothing. And in the academy especially, there's a, a tendency for everybody who specialize in medicine, for example, in healthcare. And there are so many topics, there are so many collections of symptoms, for example, one could find in healthcare that can only be seen from a multidisciplinary perspective. So you need that kind of overlap. So I just wanted to bring that up because scientists tend to be specialized. If they're really good at something, they tend to be good at one thing or one part of one thing.
And and yeah. And so somebody in in the chat says it's a compared to, compared to James's Knowledge web, I, I I love mind maps. I'm a mind map freak. The best I've seen is a closed source one from something called the Brain. I just advise people to take a look at the brain and see how it runs. And do me a favor, knock it off if you can. I mean I may be up against patents or something, but it's brilliant and as a way of exploring topics and and, and seeing what connections are between topics. But in one, you, it is open source. I'm sure that, and you may be familiar with it, but it's one that I love and it's from the Linux Foundation. It's that it's the cloud native Computing foundation landscape. Mm-Hmm. <affirmative>, it's at landscape cncf.io.
And the cool thing about it is it has, it's all a bunch of little chiclets, you know, like you see for apps in the front of your phone, but you can search some of them on off. It shows what's closed source, what's open and, and sort in a number of different ways, but it doesn't have the mapping in a way where that shows how these things connect. So I'm really looking forward to whatever you're doing with that. And if you can maybe use something from this thing, something from the brain, something from there are open source mind maps out there. Yeah. You know, where
Tim Bonnemann (00:52:15):
The, the Linux one actually I think is open source, right? We, so we
Doc Searls (00:52:18):
Actually, I'm sure it has to be.
Tim Bonnemann (00:52:19):
We, we we actually talked about that at in Vancouver and we'll definitely get check it out and see if we can even as like an interim to just get people excited about the, this idea just to just to show some initial insights. Right. so yeah. We'll, we'll, we'll, we'll definitely give it a look.
Doc Searls (00:52:39):
I think it's an awesome recruiting tool too soon as, as soon as you have, you know, a a useful visual. Yeah, an interactive visual Yeah. Of some sort. That would be great. I have a a my own question about this because AI is now in every, when I started three years ago, maybe four years ago, whatever it was on this show, which has been around for a very long time since way before podcasting was cool, <laugh>, and it was all still about, it was all blockchain and then it was all crypto. And now, right now it's it's ai and wonder if anybody in AI science is active in, in, in your work or if you're recruiting there.
Tim Bonnemann (00:53:28):
Yes. So there is a lot of AI happening in science. <Laugh>. Yeah. <Laugh>. So just, just high level, there are, you know, there are foundation models for materials. There's foundation models for biology, there's foundation models for climate right. Planetary sciences. And and I'm not an expert. I'm just very fascinated by it. There's some work that of course, you know, companies like IBM are doing that in that space. But the, the, the people we connect with also are using AI in, in their work, right? For, for, we have a bunch of computational chemists in our interest group. And so yes, it is already, it's already there. And I, I, I expect it'll only increase in importance and the, the, the speed at which things have been accelerating, especially this last past, not even a year, is just stunning. Right. And I think it'll, it'll touch everything eventually. And it's already touching the, the sciences very much. Yes.
Dan Lynch (00:54:47):
Mm-Hmm. Yeah. It it's everywhere right now, isn't it? It's, it's even gotta turn the news on and, and they're talking about, about AI's coming to take over. At some point it does seem to be accelerating. One thing I was kind of interested in a little bit, Tim, is you are you're from Germany originally. So you're originally European, like, so I am although I, like you used
Tim Bonnemann (00:55:08):
Dan Lynch (00:55:09):
<Laugh> like we used to be. Yeah, that's, I better not comment on that <laugh>. No. Yeah. Anyway, let's move on from that. But yeah I, I was interested in, obviously science is very global community and stuff. Do you see, have you found differences? Obviously you're now based in the us have you found any kind of differences in culture and stuff that affect you know, the way people approach things like development and open source and science and all that kind of stuff between say, Europe and, and North America? Maybe?
Tim Bonnemann (00:55:38):
Not yet. I look forward, I'm gonna be in Europe this summer mm-hmm. <Affirmative>, and I look forward to meeting with a bunch of people, both at some very niche conferences. I think there's two conferences related to chemistry that I'll be attending promoting open source science as a, as an opportunity and as a network. But I'm also gonna be at a bunch of more like meetups. We're gonna co-host a bunch of meetups and I'm going to be going to conferences that target more of a, the wider open source ecosystem like p Data, Amsterdam and, and a bunch of others. And look forward to learning about what the difference may differences be and the different approaches may be. It's just clear that there is a ton of energy in at least North America and Europe. And we're also currently working on our first venture into Africa. We have an opportunity to support an event in Ghana in August that's shaping up to, hopefully it's gonna come together. It looks very good. Yeah, so we're definitely globally minded. We want to you know, connect with people everywhere who are into this. Obviously like many other initiatives, you know, you, you start with a heavy North America and Europe kind of bias, but we work on expanding.
Dan Lynch (00:57:10):
Yeah, yeah, of course. And, and speaking of, of connecting and getting involved and stuff that works really well, is what I wanted to ask next is you sent us stuff about how to get involved with, with OSI F two. So if anyone's watching this, listening to this, and they think, oh, that sounds really cool, I I wanna get involved. What can they do? What should they do?
Tim Bonnemann (00:57:28):
Yeah, I just actually, I just shared this mostly in preparation for this <laugh> for this, this episode today. It's on our medium basically, at the very least. We invite you to either follow us on Medium or subscribe to our monthly newsletter, which launched this morning, when out the first inaugural issue went out just to stay in the loop, right? So we're gonna have a, you know, a a ton of things that are gonna be emerging that're gonna be announced over the next few months. Opportunities to join, you know, events in person, hybrid, virtual and probably soon opportunities to get involved hands-on with some of these open source projects that are gonna be the focus of, of some of our interest groups. And maybe also with the map, right? That's gonna need definitely hands-on developer power.
So that's at the minimum, but you can also, you can apply to join an interest group if you, if you think that's of interest. And we're gonna be, we, we started to follow up with everyone and, and we're gonna start to, you know, field them into the right groups. And there's a bunch of other options on the list. Mm-Hmm. <affirmative>. Yeah, we, you can write, I mean, so we, our medium is open for guest contributions. So if you're, if you're passionate about the intersection of open source in science and whether you are attending a conference or you, you caught an interesting, relevant session, or you have an opinion on what should be done that isn't done currently, we are generally open to give you a platform. Right. so just talk to us. We wanna, we wanna see that conversation.
And we started a just a very basic shared Google doc for people to add the events they're attending. Right. So we have a view of, cuz we can't go out to all the events, obviously, and some are very very focused to a specific discipline that, you know, we wouldn't be useful at all at these conferences. Right. but we try to facilitate people in our network knowing about these events. If they're both going, maybe meeting up, maybe they can host a meetup on our behalf, things like that. So yeah, so if you're, if you're, if you're going any of these, the list is on linked to from that post, I think. Yeah. Just to get in touch. Excellent. Yeah. Oh, sorry, doc,
Doc Searls (01:00:05):
Come on. No, I, I I was just gonna say that I, I see your, your, you run something or co-run something called C M X connects Silicon Valley, which just, just describe as a local watering hole for community types. And our family had a watering hole called the Shark and Rose on San Pedro Square in downtown San Jose at one point. That was an actual pub. Oh, nice.
Tim Bonnemann (01:00:30):
Doc Searls (01:00:30):
It is, so is this this watering hole a What is that exactly?
Tim Bonnemann (01:00:34):
Yeah, so C M X is a it's basically a community for community managers or community mm-hmm. <Affirmative> people, right. It's been around for 10 years almost, I think. Hmm. They have an annual conference in, in Redwood City back in person as of last year. So it's, it's, it's, it's been great. And they do have chapters. So I was I got involved in 2019 when they had just launched this kind of chapter for the South Bay, San Francisco, south Bay or Peninsula. And so we had a bunch of very cool meetups graciously hosted at Google that were great. And then kind of everything shut down like many other groups right. During the pandemic. And so we've been trying to get it started again. So we're working on that. We had a meet up in I think January that was super fun.
And we're working on, you know, getting it going again. It's been a bit slow but I hear that is not, that's not uncommon. It's, it's been in some cases really surprisingly hard to get people to turn out again at the same level that was kind of pre pandemic. But I also go to the Santa Cruz. So Santa Cruz started a C M X group in January. They've been, they're going strong. They have excellent monthly brunch meetings. It's been amazing, super amazing people all like community builders and weavers and gardeners and it's like super fun. So we're hoping to come up with the same four for the kind of mountain view Palo Alto, San Jose area. Excellent.
Dan Lynch (01:02:19):
And you, you mentioned that, that's, that is, that is really cool. You mentioned the, the open con o OSI is, it was only announced I think late last year or, or towards the end of, yeah, July. July, sorry. Yeah. So it's still relatively new. I mean, it is very new in, in project terms. So I, I'm wondering where you hope to be in, say, a year from now maybe, and how do you measure that success? How, how would you say, is it possible to put, you know, we want like so many interest groups, we want X amount of members. Do you guys think about that? Yeah,
Tim Bonnemann (01:02:54):
So we definitely wanna see concrete, tangible outcomes from the interest groups, right? So they're not supposed to be just, well, I guess people getting together and and getting to know each other and connecting is a, I would say is a value add, right? And, and, and good things will come from that. As a community person. I think that is a, that is a an investment that is often undervalued, right? Even though it's sometimes hard to make the concrete tieback to a, you know, dollars and cents. But we definitely want to see tangible output from these interest groups that can be shown to advance open source and science, right? So that could be something relatively simple as a, you know, an like a curated list of like open source of 1 0 1 learning resources that could be shared with professors who need to teach open source to their students, right?
Which shockingly does not always happen and doesn't always consistently exist in academia. It's just expected that young scientists or students are experts in open source at some point, even though it's not part of the the learning plan, right? So coming up with resources that would make it easier and more likely for these things to be taught at a university could be something. It could be facilitating work on concrete science related open source projects where you just see an advancement there. It could be the map, right? Mm-Hmm. <affirmative>. So we definitely wanna show we are, I think we're gonna see roadmaps or agendas or work plans coming out of these interest groups. And then we want to, you know, execute on those as much as possible. And just in terms of the community just grow it, right? So less about the number of interest groups, but the quality I think they can, they should definitely grow. There should be more people. But it's, that's gonna be about the quality and the wider community of people connected with open source science and connecting us with their existing communities, whether it's a, you know, a, a SciPi or penge or other concrete open source project that we definitely want to grow. And I think there is a lot of room to grow, so
Doc Searls (01:05:27):
That's, that's fantastic. We actually started late and then went long anyway, which is cool. We closed always with two simple questions which are possibly fun. What are your favorite text editor and scripting language
Tim Bonnemann (01:05:42):
<Laugh>? Text editor. I use, I think I use Text mate. Text mate is my mm-hmm. <Affirmative> editor. I, I'm not doing much scripting at the moment. I am learning Python though, I have to say. That is a,
Doc Searls (01:06:03):
I was thinking <laugh>, <laugh>, I was thinking since you started around Python as a project that you probably came outta that world.
Tim Bonnemann (01:06:10):
Yes. No I actually, I'm not, I'm not technical. I've been doing community for for many years. But I am diving in now. There's so many cool things that are being that well just in order to check them out, you just have to have some, and I do have some basic, but it's like, it's time to brush up and, and maybe you know, kick up, kick it up a notch. So I will be more into editors <laugh> soon. <Laugh>.
Doc Searls (01:06:40):
Yeah, it's, it, there's no right answer with any of that. But we've been wanting to get Guido fun raso on this show forever. And since he's sort of exited the python vortex, he is been loathed to involve himself with that kind of thing. But if anybody wants to light a fire under him, it'd be awesome. Meanwhile, Tim, great having you on the show. I, I, thanks
Tim Bonnemann (01:07:03):
For having me.
Doc Searls (01:07:04):
It's it's rare that we've left a number of stones unturned and you gave us a lot of them to, to prep for the show and we'll get to them next time when we have you Awesome. Back. It's sounds good. Cause obviously there's gonna be progress here.
Tim Bonnemann (01:07:16):
Thank you so
Doc Searls (01:07:17):
Much. Thanks a lot. So Dan, that was good.
Dan Lynch (01:07:23):
Yeah, great. Really, really interesting stuff. Great to talk to to Tim and, and hear about what what they're doing. I think it's a great, it's a great idea. No, I don't think any of us would, would, would complain about the idea of pulling resources to advance, you know, science and so on and, and and share knowledge and stuff. That's what we're here for. That's kind of what open source is, isn't it?
Doc Searls (01:07:43):
Yeah, it's it's funny. We could maybe ask anyway but later, but I had a friend who ran Science Commons for a while, but I haven't heard about Science Commons in a long time, so I don't know if that's still a thing or not. We can never have enough science can we <laugh> It's just this is, this is the human condition. I think it's a great topic. So we're, we're pressed for time, so give us your plug, man.
Dan Lynch (01:08:14):
Oh, right, yeah. Well people should go to dan lynch.org, which is my website, and you can find all that sort of stuff on there. There's some events coming up Liverpool Make Fest and there's one, a lo more local one called Wel Make Fest. I'll put stuff on there. Mm-Hmm. And you can find me on the Fedi verse, whatever they call it these days and Twitter and so on.
Doc Searls (01:08:32):
So did you get dan lynch.org like in 1995 or 96
Dan Lynch (01:08:37):
<Laugh>? No, I didn't, I got it late. I wanted dan lynch.com, but I couldn't get that <laugh> cause apparently there's a guy called Dan Lynch who worked with Vince Surf and some of the others in, in the creation of the internet. So he kind of got there first. And I was really gutted by that.
Doc Searls (01:08:50):
I, i, i, I wanted cirs.org, but I got srls.com, cs.org was actually around and I almost bought it, but I just didn't bother. And and I, I got that for, I got cirs.com for 75 bucks from the intern Nick I think it was, or Network Solutions, whoever it was that had that monopoly at the time. And anyway all, all these regrets, <laugh> anyway, so thanks, thanks a lot. Everybody. Oh, next week. What do we have on next week? Oh my gosh, I did not tee that one up. Okay. It's Roman tisk, T S I S Y K. He's with organic maps. We talked about maps this week. One kind of map. Let's talk about others organic maps, that's up next week, so stay tuned for that or come back for that. In the meantime, I'm Dr. Sles. This has been Floss Weekly. We'll see you then.
Leo Laporte (01:09:45):
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