Could Proton save academics from closed source software? [circular rant and doubts abound]

Communities Blog
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Hi!

First of all, apologies if this is not in the right section of the forum: it’s not a request for an how-to, just a bit of a rant and a spiel about a very niche niggle on the road to moving to Linux.

Core Question: Pronton has allowed us to finally get more games on Linux and I’m personally ecstatic about it. But could Proton be used for other uses beside gaming? Isn’t it at it’s core a wine sort of tool? Could it be used to run generic windows software? Dare we say, could it run the dreaded academic dyarchy Endnote/MSWord? Have I completely misunderstood what Proton is?

Here lies my deeply overcomplicated, hyper-niche, totally irrelevant in the grand scheme of things first world conundrum, o weary traveller of this forum: sit a while, let’s sacrifice some dark wine to the shadows and let’s talk circularly about what could or could not be.

So my day job is on the research side of academia, in the humanities: since 2013 I’m still the only person in my circle to use a reference manager software. All my younger and older colleagues, supervisors and so on deal with referencing by hand. Actually, I have bosses who believe manually color coding excel cells is a way of cataloguing information… Yeah, I still shudder. Moving on.

Unfortunately I started using EndNote (on windows) during my PhD as my reference manager and I’ve grown to rely on it quite heavily: I learned the tool, especially the custom reference style editing gui, which has been of great use.

Clarivate has expressed its complete lack of interest in making their software linux compatible: they are moving parts of the software to the browser, but it’s a way to lead you to save your databases in their cloud so you can reference your stuff in online text editors. Not exactly a fan, but I get that’s the closest I could get to OS agnostic from this software house.

I’m thinking about getting a new thinkpad with Stryx Point and I’d like to take the chance to move to Fedora instead of Windows 11, but then EndNote/Word is the only piece of software I really need to work form day one (one and a half max) and it seems to force me to stick with MS.

I’ve been trying out alternative software combinations: the one I liked the most is Zotero+LibreOffice. I love the openness of Zotero and LibreOffice looks really polished, the integration between the two works OK, but the CSL format for custom styles is really convoluted form me. Powerful, but knowing me I would need to master it to fix issues that will inevitably come up and that’s not something you really want when you’re in the grips of peer review and impostor syndrome.

I know dual booting or VMs are a thing, but switching back to Windows for work stuff, it feels a bit of a convoluted.

So, theoretically, could Proton be an answer in the future? Without getting into licensing grey areas, could it run EndNote and it’s integrations with word processors on Linux (not necessarly MS Word of course)? Would the software in question need to be altered to work with Proton?

Have I just wasted a bucket load of your time to ask a stupid theoretical “what if?” question? Probably… I’m sorry, here’s a flower for your trouble: :blossom:.

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You don’t want proton, you just want plain old Wine.

According to wineappdb, endnote already works: https://appdb.winehq.org/objectManager.php?sClass=application&iId=835

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Hi!

I would be so happy if it were so, but it really doesn’t work. Oh, it installs and it starts, don’t get me wrong, but that’s about it.

I submitted my most recent test I ran to wineHQ just to show that the silver rating it got is misleading (it should be up momentarily). The program won’t CWYW, it has some graphic issue, it hangs… I mean, it already fantastic that is starts IMHO, but it’s really not usable.

My hope was that Proton could bring more eyes on compatibility software and on wine itself, thus allowing more refinement in this sort of “transitionary” situations. Of course, Wine does what it can, I was already surprised that endnote would launch.

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If I understand correctly, and I possibly don’t since I’m just parroting what I’ve read rather than having anything to do with actually developing these tools, there’s really nothing Proton is doing that isn’t just some flair with the packaging… You can get dxvk and all that jazz going with vanilla wine, it just takes winetricks and whatnot.

You might check out “bottles” - you can pretty easily set up a wine environment where you might get it working properly.

I haven’t had any luck with several products, myself, lately - bluebeam, autodesk products, etc. It might be possible to get some of them going, but I think it’ll take some developer effort for many of these things, and on others (autodesk) they’re actively hostile to running it anywhere but windows.

I ended up keeping a win10 VM handy on my server that I can just ssh through for bluebeam or whatever.

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BibTeX?

That would explain the (over?)reliance on Microsoft products; word on campus(es of the world) is that researchers outside of maths, physics, and computer science don’t tend to know (La)TeX.

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I tried bottles! I might give it a go for my use, although if Wine has worked as it did.

I’ll probably have to rely on a VM if I’ll switch one laptop to Fedora, but probably I’ll just bite the bullet and learn to style Zotero’s way…

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Hi!

Absolutely true. Latex/Bibtex is not really a thing here, I’ve never met a single person using bibtex or latex . It’s probably down to the publishing and journals, they all require docx and refuse typesetted material like the plague. Also, the need to have a precisely typresetted document is less when all you have is just text and a few automated fields for references (which you need to turn into plain text or the journal will refuse it).

I think the one time I mentioned latex to someone they thought I was talking plastic you wear.

Since my phd I saw the universities and research institutes became “Microsoft only”, ditching even Google because faculty really didn’t get along google docs for example.

Also, it’s an inkling to why no one uses reference managers: MS doesn’t have one in its suite, unless you want to call the bibliography tool in word that.

It’s a sad state, outsourcing all services over to MS for public universities and railing everyone who has to deal with faculty or research force into MS. And to think there’s a law in my county that public services should adopt open standards and open software: turns out it’s more expensive to train people to use free non-MS suites than to give them MS suites.

Anyway, sorry for the OT: I’ll have a look into how BibTex deals with custom reference styles, maybe I can use it. Thanks!!

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I used bibtex+latex in my old uni life. I’m not going to try to sell you on it. Just as I hope you won’t try to sell me on endnote+word :slight_smile:

I think breaking out from proprietary software, formats and ecosystems is a noble goal, especially in the (commonly tax payer funded) education sector.

But I think if you never leave endnote you are as much of an obstacle in achieving that goal as anyone else.

The docx being the expected/enforced format for document interchange is the most difficult part to change since you don’t set those rules - personally I’ve managed to make do with openoffice’s export when I was in uni but I wonder if that’s still viable. Now days I just don’t interact with anyone/anything that requires MS Office or Windows. I’ve skipped over plenty of jobs because they only accepted .doc files. Who knows what potential better life I could have had!

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Microsoft software will not work in Proton or wine so if you want office you need Windows. The good news is that it is easy to spin up a Windows VM and you can use the qemu guest tools to enable acceleration, shared clipboard and automatic resizing. Basically what you would want to do is create a Windows VM in virtual manager with the guest tools installed and then open up word to full screen. This way you can use the host apps along side word in a VM. You can copy and paste things in and out and the screen dynamically resizes.

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Ditto - every now and again I try to use something other than Outlook. However, I can’t deal with Thunderbird

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That’s likely because, like a good predator, MS sweeten their offers for academia to lock in all these future victims that will pay them millions more a few years down the line.

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I’d never try to impose that on another living creature! Nor I think I could, since it’s the system I’m trying to get out of :wink:. I would actually like to play with something new! (it would give me a great excuse to further delay actually writing).

It’s actually very effective, libreoffice works in docx and it’s easy to use MS fonts to avoid the docs being exchange with MS suites looking wonky. Documents and spreadsheet (without macros) seem to “move” pretty well.

I agree, as in many of such endevours. I get the small personal satisfaction of trying, at least, and being aware of the wider scope of the attempt.

It would probably make my work parasocial life so much better.

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Absolutely,

I’ve been running Debian VMs on my server for years and I use a Win11 vm as a sandbox on my WIn11 desktop.

Until now the issue was that my laptops were a bit to… emh… let’s say “lean” to effectively run a WIN Vm all the time, since on a laptop the vast majority of what I do is actually within Office+EndNote and some such. With new hardware it could be a simple thing if I really can’t switch all at the same time.

That’s why I’ve not given up on a complete move from Endnote+Work to Zotero+Libre or getting on board the TeX system.

This feels like learning a new language: it’s a progression and some crutches are needed sometimes.

Still, I really hope that with the attentions that this new translation layers are getting in general, we might be moving to a more OS agnostic way of making software. A pipe dream, for sure, but one can hope.

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So, let’s take a look at your requirements: Fedora, Win legacy stuff to work on day one because you need it for work.

I recommend getting a dual monitor setup (in case you don’t have that already) - I think it’s unbeatable for productivity (except maybe for triple, quad, … I digress).
Install Windows plus any tool you need in Box on Fedora which works without prayers. You max the box window on one screen, you work in Linux native apps on the other, your mouse, clipboard, focus changes as you expect. If you pick the right background in Windows you won’t even notice it’s there.

This will give you all the time in the world to figure out the depths of wine. Plan on a long time. I use Fedora as a daily driver for a couple of years, generally Linux for 30+. I cannot figure out wine.
That’s why there are so many apps that promise to make wine work (Proton, Lutris, etc.).

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Shameless copy pasta from another thread asking about VERY specific software being virtualized:

Been there, did it

if you want to run locally:
QEMU
Windows 11 pro VM (you’ll need a rufus modded Win 11 iso to bypass TPM and hardware requirements)
strip of the BS and nerf the install to the bare basics
install software
host SMB share from Windows VM
mount SMB share in Linux and map locally for file transfer

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sauce: Sage 50 Accounting Canadian Edition under Wine on Linux - #15 by Taylor_Goehring

I have to virtualize legacy software all the time
This is how we prefer to on linux machines

if you’ve got TPM pass through enabled, even better. But honestly I do not recommend it as having that portable VM is worth something.

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Thanks for the advice! I’m so dependent on dual screens (or big ones) that I carry a usb monitor with me any time I move away for research. Can’t function without it.

You’re giving me lots of confidence, I’m going to try it this way. It would give me time to learn linux native Zotero in the interim.

Thanks!

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Thanks for the link! It seems that VMing is something that can help me ferry my workflow. I did virtualize Win plenty of times, I’ll look into using the more strip down versions of it.

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It’s also possible to use an emulated TPM. Probably easier and less error prone.

On another note, would it be possible to use the online version of word? Office 365? It’s definitely not preferred in some ways since it’s a prescription service, cloud only, but perhaps an option?

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This.

Also, FYI a lot of the fixes that were initially made in proton have been backported to wine.

Think of proton as a valve funded, bleeding edge, gaming focused version of wine, because that’s basically what it is. Valve have been focused exclusively on making games work, where regular wine has been trying to make applications in general work with a different set of trade-offs.

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