good practices in science

good practices in science

[Marco van Hulten]

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 has been growing over the years, and getting a
spurt during the COVID-19 pandemic (maybe not unlike 9/11).  Examples
include that here at the university we are expected to use Zoom and
Skype, and this was a good moment to push through Microsoft Teams (as a
"good replacement for mail").  These are all tools that are not open
spec, free software or federated.  Very few of my collegues care, and
those that do have the opinion (or understanding) that it is too late
to do something about it.

At the University of Bergen it is expected that we install and use
proprietary software on our home network (e.g. MS Teams, Skype and Zoom
– two of these run luckily in Chromium).  Except for the integrity of
our scientific results, our privacy and general home security is
affected.  We have to find ways to mitigate the situation (e.g. laptop
dedicated to all the crap on a special subnet).  But, in my opinion,
such mitigations should not even be necessary in the first place.
Especially in an environment of learning and research things should be
really different.

There are related, even worse, issues outside of academia, like the
proprietary COVID-19 tracking apps that several countries are building,
mostly independently because "we cannot trust another country's app"
(which would be moot point if ...).  Discussion of these wider issues
would warant a forked or separate thread (or perhaps a different
mailinglist).  I think it's all connected, but now I'd like to focus on
free software and science.


When I do science (the ordering and creation of concepts, models,
hypotheses and theories; through thinking, programming, simulating,
evaluating, discussing and writing), I have a way of working that I
think is efficient and in line with the scientific method.  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.

But it doesn't work like this.  Collegues don't follow this workflow,
and they don't care about freedom.  They actually think that Track
Changes is the same as version control management.  I have some
work-arounds for the incompatibility between the workflows.  For
instance, I write most things in Markdown and use pandoc(1) to convert
it to PDF and ODT.  The collaborators may use any method to comment on
my text and then send it back.  They never edit the source, they almost
invariably send back a (non-strict OOXML) docx with Track Changes or a
PDF with text balloons.

In academics, there was recently (in Norway just a year ago) a
discussion about open access.  The discussion showed that it is very
difficult for my collegues to only publish open access – they consider
it as a serious problem, even though I would not think twice to publish
a paper that restricts its readers.

For writing papers I tried the proprietary service Overleaf (and
similar) or sending the TeX files, but it doesn't work.  They won't use
it.  They even copy text from a PDF into MS Word and send a Track
Changed document in a top-posted HTML e-mail back to me.  Some of them
expect me to do the same thing (or using Google Docs or Sharepoint or
so; sometimes logging in is expected as well).

For anyone writing a thesis and having these problems right now: don't
think they will go away.  It does not even matter if you have your own
funding.  Most of your partners won't care about anyone's freedom, and
you still have to find ways to work with their inefficient workflows.

Free software helps a lot dealing with this, but these inefficiencies
are not necessary.  The inefficiencies arise from naivity about free
software and technology, or just not caring and/or trying to follow
status quo and writing senseless proposals (with inefficient and
non-free tools).

This is the state for Earth sciences.  My work is appreciated in my
field, so I might survive in the system (writing proposals and crap),
but these unnecessary inefficiencies are *at least* an annoyance, and
it does not appear to get any better.

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?

I am considering going out of science and focus completely on free
software development, even though I have a slight preference of keep on
doing science.  The switch would for a large part be based on the fact
that a different workflow (set of tools) is used for free software
development compared with science.  Is it crazy to choose your career
path based on the tools the people of the respective field is using?

If the community of Earth scientist free software users does not exist,
is it better in other scientific fields?  I guess it may be better in
physics, astronomy and some parts of biology, but it will be far from
perfect because also the other departments need to live with the
universities' policies, right?


I realise that I am privileged in even potentially have the option to
change my career path, and that a not so unreasonable answer would be
"shut up and live with it".  But I still also appreciate any other kind
of advice.  :-)

—Marco

Re: good practices in science

[Pjotr Prins]

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.

Re: good practices in science

[Pierre Neidhardt]

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Hi Marco,

Great write up!
I think you should publish this and spread the word.
Every little bit helps!

> Is it crazy to choose your career
> path based on the tools the people of the respective field is using?

Maybe, but that's one of the key reasons I dropped academia and the
corporate world :)

Cheers!

-- 
Pierre Neidhardt
https://ambrevar.xyz/

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Re: good practices in science

[Konrad Hinsen]

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

[Cook, Malcolm]

> 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

[Pierre Neidhardt]

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> 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/

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Re: good practices in science

[Marco van Hulten]

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

[Bijan]

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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 has been growing over the years, and getting a
> spurt during the COVID-19 pandemic (maybe not unlike 9/11).  Examples
> include that here at the university we are expected to use Zoom and
> Skype, and this was a good moment to push through Microsoft Teams (as a
> "good replacement for mail").  These are all tools that are not open
> spec, free software or federated.  Very few of my collegues care, and
> those that do have the opinion (or understanding) that it is too late
> to do something about it.
>
> At the University of Bergen it is expected that we install and use
> proprietary software on our home network (e.g. MS Teams, Skype and Zoom
> – two of these run luckily in Chromium).  Except for the integrity of
> our scientific results, our privacy and general home security is
> affected.  We have to find ways to mitigate the situation (e.g. laptop
> dedicated to all the crap on a special subnet).  But, in my opinion,
> such mitigations should not even be necessary in the first place.
> Especially in an environment of learning and research things should be
> really different.
>
> There are related, even worse, issues outside of academia, like the
> proprietary COVID-19 tracking apps that several countries are building,
> mostly independently because "we cannot trust another country's app"
> (which would be moot point if ...).  Discussion of these wider issues
> would warant a forked or separate thread (or perhaps a different
> mailinglist).  I think it's all connected, but now I'd like to focus on
> free software and science.
>
>
> When I do science (the ordering and creation of concepts, models,
> hypotheses and theories; through thinking, programming, simulating,
> evaluating, discussing and writing), I have a way of working that I
> think is efficient and in line with the scientific method.  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.
>
> But it doesn't work like this.  Collegues don't follow this workflow,
> and they don't care about freedom.  They actually think that Track
> Changes is the same as version control management.  I have some
> work-arounds for the incompatibility between the workflows.  For
> instance, I write most things in Markdown and use pandoc(1) to convert
> it to PDF and ODT.  The collaborators may use any method to comment on
> my text and then send it back.  They never edit the source, they almost
> invariably send back a (non-strict OOXML) docx with Track Changes or a
> PDF with text balloons.
>
> In academics, there was recently (in Norway just a year ago) a
> discussion about open access.  The discussion showed that it is very
> difficult for my collegues to only publish open access – they consider
> it as a serious problem, even though I would not think twice to publish
> a paper that restricts its readers.
>
> For writing papers I tried the proprietary service Overleaf (and
> similar) or sending the TeX files, but it doesn't work.  They won't use
> it.  They even copy text from a PDF into MS Word and send a Track
> Changed document in a top-posted HTML e-mail back to me.  Some of them
> expect me to do the same thing (or using Google Docs or Sharepoint or
> so; sometimes logging in is expected as well).
>
> For anyone writing a thesis and having these problems right now: don't
> think they will go away.  It does not even matter if you have your own
> funding.  Most of your partners won't care about anyone's freedom, and
> you still have to find ways to work with their inefficient workflows.
>
> Free software helps a lot dealing with this, but these inefficiencies
> are not necessary.  The inefficiencies arise from naivity about free
> software and technology, or just not caring and/or trying to follow
> status quo and writing senseless proposals (with inefficient and
> non-free tools).
>
> This is the state for Earth sciences.  My work is appreciated in my
> field, so I might survive in the system (writing proposals and crap),
> but these unnecessary inefficiencies are *at least* an annoyance, and
> it does not appear to get any better.
>
> 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?
>
> I am considering going out of science and focus completely on free
> software development, even though I have a slight preference of keep on
> doing science.  The switch would for a large part be based on the fact
> that a different workflow (set of tools) is used for free software
> development compared with science.  Is it crazy to choose your career
> path based on the tools the people of the respective field is using?
>
> If the community of Earth scientist free software users does not exist,
> is it better in other scientific fields?  I guess it may be better in
> physics, astronomy and some parts of biology, but it will be far from
> perfect because also the other departments need to live with the
> universities' policies, right?
>
>
> I realise that I am privileged in even potentially have the option to
> change my career path, and that a not so unreasonable answer would be
> "shut up and live with it".  But I still also appreciate any other kind
> of advice.  :-)
>
> —Marco
>

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Re: good practices in science

[Pierre Neidhardt]

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Bijan <ghavamikia@hotmail.com> 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/

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Re: good practices in science

[Bijan]

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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 <mail@ambrevar.xyz> wrote:
>Bijan <ghavamikia@hotmail.com> 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.

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Re: good practices in science

[Konrad Hinsen]

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

[Bengt Richter]

On +2020-04-06 10:18:33 +0200, Pierre Neidhardt wrote:
> Bijan <ghavamikia@hotmail.com> 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:underlay@media.mit.edu
    6. in Underlay - fn5
    7. http://kfg.mit.edu/
    8. mailto:underlay@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:consortium@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:consortium@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

[Bengt Richter]

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

[Konrad Hinsen]

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

[Bengt Richter]

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

[bijan ghavami-kia]

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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.hinsen@fastmail.net>
Sent: 07 April 2020 09:40
To: Bengt Richter<mailto:bokr@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.


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RE: good practices in science

[Konrad Hinsen]

bijan ghavami-kia <ghavamikia@hotmail.com> 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

[Pierre Neidhardt]

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bijan ghavami-kia <ghavamikia@hotmail.com> 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/

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