Re: good practices in science

[Bijan]

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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