RE: good practices in science
bijan ghavami-kia writes: > Oh my goodness, I didn’t know who Danny Hillis was before a google search..., > except I did because the way I heard about this project first was from him! > https://www.youtube.com/watch?v=YmF7KvsldGU Very nice video, thanks for sharing! -- Pierre Neidhardt https://ambrevar.xyz/ signature.asc Description: PGP signature
RE: good practices in science
bijan ghavami-kia writes: > It’s an interesting prospect, shouldn’t we be working towards this > fantastical goal? We (Guix) are already working towards the abstract goal of this project, because what Guix does is effectively provenance tracking for computations. Guix' package dependency graph is part of the public knowledge graph. If and how we could collaborate with the Underlay in a more institutional and technical sense is an interesting question to think about. One ingredient mentioned by Underlay is IPFS, with which Guix has already made contact. And IPFS is looking into including git repositories by providing CIDs for Git commits (though this doesn't seem high-priority task). Guix is already connected to the Software Heritage archive (two ways: Guix is archived there, and it can work with source code from the archive), which is basically Git scaled up massively. All that means that hooking up Guix with the Underlay is a pretty straightforward endeavor from a technical point of view. It's mainly a question of all interested parties agreeing on some form of collaboration. So we are back to politics! Personally I'd love to see this happen, and I'd definitely be willing to participate actively. Cheers, Konrad
RE: good practices in science
Oh my goodness, I didn’t know who Danny Hillis was before a google search..., except I did because the way I heard about this project first was from him! https://www.youtube.com/watch?v=YmF7KvsldGU A good salesman! I’m embarrassed I brought it up! It’s an interesting prospect, shouldn’t we be working towards this fantastical goal? From: Konrad Hinsen<mailto:konrad.hin...@fastmail.net> Sent: 07 April 2020 09:40 To: Bengt Richter<mailto:b...@bokr.com> Cc: guix-devel@gnu.org<mailto:guix-devel@gnu.org> Subject: Re: good practices in science Hi Bengt, > (I guess I get excited reading prose that shows attention > to the distinction between abstractions and their representations. > Sort of like reading quotes from Plato, and thinking, "Hey, wow, > I've had some of those thoughts." :) There are plenty of good ideas in that project, I am not claiming the opposite. Unfortunately, that has never been a guarantee for success. > I hope they are not just preparing themselves for spinning off > and becoming rich as a monopolist takeover target ;-/ With people like Danny Hillis on board, they should be aware of that trap! > So what makes you hopeful about guix? :) It's so technical that politics-minded people won't even look at it. Cheers, Konrad.
Re: good practices in science
Hi Konrad, > > So what makes you hopeful about guix? :) > > It's so technical that politics-minded people won't even look at it. LOL :)) -- Regards, Bengt Richter
Re: good practices in science
Hi Bengt, > (I guess I get excited reading prose that shows attention > to the distinction between abstractions and their representations. > Sort of like reading quotes from Plato, and thinking, "Hey, wow, > I've had some of those thoughts." :) There are plenty of good ideas in that project, I am not claiming the opposite. Unfortunately, that has never been a guarantee for success. > I hope they are not just preparing themselves for spinning off > and becoming rich as a monopolist takeover target ;-/ With people like Danny Hillis on board, they should be aware of that trap! > So what makes you hopeful about guix? :) It's so technical that politics-minded people won't even look at it. Cheers, Konrad.
Re: good practices in science
Hi Konrad, On +2020-04-06 17:09:14 +0200, Konrad Hinsen wrote: > Hi Pierre, > > > I had never heard about this project, looks like it's a most critical > > venture these days! :) > > > > https://underlay.mit.edu/ > > > > Any idea if there is a public project page? > > My understanding is that the project just started and hasn't much to > show for now. It's on my "have-a-look-every-three-months" list. > > The real question with this type of infrastructure project is if it will > produce something convincing enough for many players to adhere to. It's > as much politics as technology. That sounds sad. Maybe I got overexcited ;-/ (I guess I get excited reading prose that shows attention to the distinction between abstractions and their representations. Sort of like reading quotes from Plato, and thinking, "Hey, wow, I've had some of those thoughts." :) I hope they are not just preparing themselves for spinning off and becoming rich as a monopolist takeover target ;-/ Or that they're looking forward to being raided by offers of signing bonuses and a playground with expensive toys, just to keep their competition out of the market. Or that they'll be disrupted by metoo accusations. So what makes you hopeful about guix? :) > > Cheers, > Konrad > -- Regards, Bengt Richter
Re: good practices in science
On +2020-04-06 10:18:33 +0200, Pierre Neidhardt wrote: > Bijan writes: > > > I look forward to when the existing infrastuctures are further > > strained when we hopefully get open access papers (and other > > knowledge) distributed in a decentralised way eg on IPFS, if this were > > feasable, [I saw some ideas about this coming from the MIT 'underlay' > > project (basically a knowledge graph on ipfs)]. > > I had never heard about this project, looks like it's a most critical > venture these days! :) > I hadn't heard either, thanks! > https://underlay.mit.edu/ > > Any idea if there is a public project page? > > -- > Pierre Neidhardt > https://ambrevar.xyz/ Just chase the links, Luke ;-) (I used lynx -l to get the links for this) (from the above URL: --8<---cut here---start->8--- References in https://underlay.mit.edu/ 1. in Underlay - fn1 2. in Underlay - fn2 3. in Underlay - fn3 4. in Underlay - fn4 5. mailto:under...@media.mit.edu 6. in Underlay - fn5 7. http://kfg.mit.edu/ 8. mailto:under...@mit.edu 9. in Underlay - sup1 10. in Underlay - sup2 11. https://unstats.un.org/unsd/demographic-social/products/vitstats/sets/Series_A_2011.pdf 12. in Underlay - sup3 13. https://www.news24.com/World/News/Discontent-over-Sudan-census-20090521 14. in Underlay - sup4 15. in Underlay - sup5 16. https://www.cisco.com/ --8<---cut here---end--->8--- # 7. is http and forwards to https://www.knowledgefutures.org/ https://www.knowledgefutures.org/ gets you lots of goodness: --8<---cut here---start->8--- References in https://www.knowledgefutures.org/ 1. in Knowledge Futures Group 2. https://www.knowledgefutures.org/about 3. https://www.knowledgefutures.org/jobs 4. https://www.pubpub.org/ 5. https://www.underlay.org/ 6. https://commonplace.knowledgefutures.org/ 7. https://2019.knowledgefutures.org/ 8. https://twitter.com/kfutures 9. https://eepurl.com/gJzIjD 10. https://www.knowledgefutures.org/jobs --8<---cut here---end--->8--- ...of which #5 gets you --8<---cut here---start->8--- References in https://www.underlay.org/ Visible links: 1. in Underlay RSS Feed 2. in Underlay 3. in Underlay - main-content 4. https://www.underlay.org/search 5. https://www.underlay.org/login?redirect=/ 6. https://www.underlay.org/pub/tdefqg1q 7. https://eepurl.com/gJL39b 8. https://www.underlay.org/pub/tdefqg1q 9. https://www.underlay.org/pub/le752275 10. https://www.underlay.org/pub/future 11. mailto:consort...@underlay.org 12. https://www.knowledgefutures.org/ 13. in Underlay 14. in Underlay RSS Feed 15. https://www.underlay.org/legal 16. https://www.pubpub.org/ Hidden links: 17. https://www.underlay.org/project 18. https://www.underlay.org/protocol 19. https://www.underlay.org/underlay.org 20. mailto:consort...@underlay.org --8<---cut here---end--->8--- Don't miss the white paper! (link 10) ;-) Byline: by Danny Hillis, Samuel Klein, and Travis Rich The philosophy of the Underlay. (is that the Connection Machine Hillis?) Nor miss 12 and 16 Really exciting: Maybe idealism will go viral :) Though I'm pretty sure I'm not comfortable with script-kiddies [1] getting too easy access to knowledge they are not mature enough to handle ;-/ Amateur Jurassic Parks, anyone? Oops, that became a virus, not a tame T-Rex we can ride, what shall we do? [1] Not to mention Scrooge amd Dr.Strangelove ;-/ -- Regards, Bengt Richter
Re: good practices in science
Hi Pierre, > I had never heard about this project, looks like it's a most critical > venture these days! :) > > https://underlay.mit.edu/ > > Any idea if there is a public project page? My understanding is that the project just started and hasn't much to show for now. It's on my "have-a-look-every-three-months" list. The real question with this type of infrastructure project is if it will produce something convincing enough for many players to adhere to. It's as much politics as technology. Cheers, Konrad
Re: good practices in science
I'm not sure I think this is their git hub repo after a quick search, https://github.com/underlay,... might be worth looking at 'solid' mit project, Im not sure but I think it shares similar underlying infrastructure with linked data structures on ipfs. On 6 April 2020 09:18:33 BST, Pierre Neidhardt wrote: >Bijan writes: > >> I look forward to when the existing infrastuctures are further >> strained when we hopefully get open access papers (and other >> knowledge) distributed in a decentralised way eg on IPFS, if this >were >> feasable, [I saw some ideas about this coming from the MIT 'underlay' >> project (basically a knowledge graph on ipfs)]. > >I had never heard about this project, looks like it's a most critical >venture these days! :) > >https://underlay.mit.edu/ > >Any idea if there is a public project page? > >-- >Pierre Neidhardt >https://ambrevar.xyz/ -- Sent from my p≡p for Android. pEpkey.asc Description: application/pgp-keys
Re: good practices in science
Bijan writes: > I look forward to when the existing infrastuctures are further > strained when we hopefully get open access papers (and other > knowledge) distributed in a decentralised way eg on IPFS, if this were > feasable, [I saw some ideas about this coming from the MIT 'underlay' > project (basically a knowledge graph on ipfs)]. I had never heard about this project, looks like it's a most critical venture these days! :) https://underlay.mit.edu/ Any idea if there is a public project page? -- Pierre Neidhardt https://ambrevar.xyz/ signature.asc Description: PGP signature
Re: good practices in science
Hi Marco, agree this isn't the forum (so I apologies for adding more to the disussion), but I sympathize with your view, I'm not a natural scientist, about as far from it, I'm a physician, who are generally as different from academics as physicians are from surgeons. I work as an infectious diseases doctor in the UK and have no programming experience worth talking about, though I do aspire to if there was more time in the day and more space in my brain. IMO there's multiple factors that stop people from using free open software, my own 'journey' into this arena is completely wayward and probably indicative of general ignorance that contributes to this; I started using as a student ubuntu back in the 'golden era' of ubuntu, pre-unity etc, purely because it was free (as in beer) and easy to use and I was curious about this concept of a community contributed project (I don't remember how I came across it), this led to discovering what the open source world is and how concepts are applicable to non-programming areas; the licenses, the funding issues, security issues etc; eventually someone mentioned R and open statistical software for research; this then led to TeX, Knuth and the concepts of literate programming being applied to research papers; proliferation of open software with educational supports (Datacamp etc), new languages (julia), and platforms for development (eg jupyter), [even the public health england website advocates to use open released data with R], proliferation of open access journals in the last 10 years, bioRxiv and medRxiv for prepublication repositories and the reevaluation of the peer review process (see pubpeer as an interesting example); as a live example of why we need open access, all the proprietary journals eg NEJM, release their covid research for free (a temporary feature that should ideally1 be permanent). somehow I was led to guix and although I don't know coding I (hopefully) recognise good principles and with guix the necessity of not just code but the reproducible and bootstrapped environment as being important. Maybe I'm optimistic, all this may not translate to day to day all the time, but the fact this exists in the world at all gives me great joy. It's not perfect and it's a work in progress for sure but compared to 15-20 years ago I feel things have moved on (I'm referring to the medical field, which is notoriously, sadly, behind in the many concepts that have long existed in other fields of modern research). I look forward to when the existing infrastuctures are further strained when we hopefully get open access papers (and other knowledge) distributed in a decentralised way eg on IPFS, if this were feasable, [I saw some ideas about this coming from the MIT 'underlay' project (basically a knowledge graph on ipfs)]. Apologies for the ramble and poor writing and incoherence in the inappropriate forum, what I wanted to highlight was how easily non of this may have been known to me; I agree with Pjotr, do what you enjoy, if you want to do something, provide education materials so that people come into this area with more deliberation than the almost accidental haphazard way I stumbled into it. I am very hopeful like Piotr about the situation, everywhere there are wins and your frustrations I feel are a signal of those wins! Pjotr for my own interest (because I don't think I will be able to contribute) what is your biohackathon about and where can I find information? On 03/04/2020 14:00, Pjotr Prins wrote: > Dear Marco, > > I don't think this is the place to discuss the ins and outs of > science. The scientific community and arena can be frustrating and I > would say (i.e., as an opinion) that you should only work in science > if the subject itself grabs you. I left the software industry for > biology 15 years ago and have not looked back. I love my work. > > We are organizing a COVID-19 biohackathon coming week for free > software and free data. Feel free to watch and join. We are > using some proprietary tools - usually they come with lab protocols - > such as sequencers - though for me I try to avoid them as much as > possible, and we can create free alternatives. But overall I am pretty > happy with what I can do in science with free software and I only > write free software! Let free software rule. > > I am excited about free hardware developments and Linux phones. > Hopefully we'll get GNU Guix on those soon. > > Pj. On 03/04/2020 12:54, Marco van Hulten wrote: > Hi all— > > Are there any natural scientists here? I'm asking because at least in > my field not the right tools are used to do the work; I'd like to > exchange ideas on how to approach these issues. I am sending this to > this list because Guix is an obvious tool for scientific (and other) > computing. None of my collegues anywhere in the world have heard of it > and they are not interested when I mention it. (Furthermore, brendyyn > on #guix suggested this list.) > > > Invasion of privacy
Re: good practices in science
Hello— Thank you all the useful comments. I believe that these tips can really help me with my further career. Even as this list's purpose is not to ask personal advice, I am happy that I did ask here. Strangly, I could not get this insight by talking about it with collegues, friends and family (I tried). A main message I got here is that even if things look grim (concerning technology), there are good initatives and people that are improving the situation, or at the very least that there are opportunities out there that can make one's personal and career situation better. Best, take care, —Marco
Re: good practices in science
> It is growing. I can't say about your field or your neigbourhood, but > check out communities such as The Carpentries > (https://carpentries.org/), which is organizing tutorials all around the > globe to teach the tools that you like. I had never heard about this initiative before, this is great! Thanks for sharing! -- Pierre Neidhardt https://ambrevar.xyz/ signature.asc Description: PGP signature
Re: good practices in science
> I would like to find a community where I can do science in a good way. > I want to use free software and would like to collaborate through > version control, IRC, Jitsi, well formatted e-mails. Does such a > community exist? Look into [Center for Open Science](https://cos.io/) I the R world, there is [rOpenSci](https://ropensci.org/about/)
Re: good practices in science
Hi Marco, > Are there any natural scientists here? I have no idea how numerous we are, but yes, there are. As for myself, I am in computational biophysics. > I am sending this to this list because Guix is an obvious tool for > scientific (and other) computing. None of my collegues anywhere in > the world have heard of it and they are not interested when I mention > it. (Furthermore, brendyyn on #guix suggested this list.) Don't worry, that will change. > In my mind, this must mean that one writes plain text everywhere. > This is plain/text for e-mail, LaTeX for papers, code is code, > Markdown or similar for most other documents. All this is in version > control. You can push, share, collaborate quite easily. Anyone is > free to make a pretty PDF of it or do whatever else. Because, of > course it is all free as in speech. You know all this. That is a workflow which is being advocated increasingly. You could point your doubting colleagues to this MOOC, for example: https://www.fun-mooc.fr/courses/course-v1:inria+41016+self-paced/about (disclaimer: I am one of its authors). Guix is not covered there, but it will in a more advanced sequel currently under preparation. > I would like to find a community where I can do science in a good way. > I want to use free software and would like to collaborate through > version control, IRC, Jitsi, well formatted e-mails. Does such a > community exist? It is growing. I can't say about your field or your neigbourhood, but check out communities such as The Carpentries (https://carpentries.org/), which is organizing tutorials all around the globe to teach the tools that you like. Cheers, Konrad
Re: good practices in science
Dear Marco, I don't think this is the place to discuss the ins and outs of science. The scientific community and arena can be frustrating and I would say (i.e., as an opinion) that you should only work in science if the subject itself grabs you. I left the software industry for biology 15 years ago and have not looked back. I love my work. We are organizing a COVID-19 biohackathon coming week for free software and free data. Feel free to watch and join. We are using some proprietary tools - usually they come with lab protocols - such as sequencers - though for me I try to avoid them as much as possible, and we can create free alternatives. But overall I am pretty happy with what I can do in science with free software and I only write free software! Let free software rule. I am excited about free hardware developments and Linux phones. Hopefully we'll get GNU Guix on those soon. Pj.
