Re: [O] General advice beyond Org
On Wed, Jun 6, 2018 at 3:58 AM, Marco wrote: > I started as post-doc almost 10 years ago, Thanks for your share Marco.
Re: [O] General advice beyond Org
Hey fellow orgers, I started as post-doc almost 10 years ago, I made a point in having linux on my desktop and only use software I see fit - and know - such R, and LaTeX to write papers. The occasional word/excel document I opened with libreoffice/wps office or more frequently remotely on a windows server / on a virtualbox, same with the occasional windows-only piece of software I needed to use. After 8-9 years of mockery, my whole departement is now switching to LiNuX/LaTeX/python/R/jupyter, with the exception of a few specialized softwares which are windows-only and will run on selected machines/servers. Point is, also the secretary has to migrate, she was the greatest advocate against the change. No luck yet with emacs + org with my colleagues, but hey, one step at a time ;) If your research and daily work involves programming/modelling I actually don't see any point in staying on windows. Unices have LOTS of advantages. The best general-purpose research tools nowadays are free/libre software (since 3D FEM was named: openfoam, moose, opencascade/salome, code_aster just to name a few... ), that is, if you are developing something and not just running models, their steep learning curve pays off immediately. If it's just a matter of running specific models maybe there are other specialized softwares which may be more efficient (e.g., avizo for 3D microtomography, eclipse / petrel for geological modelling and reservoir engineering). In the realm of statistics/machine learning/AI it's all linux-based free software (think about keras + tensorflow with R and Python, but loads and loads of other similar stuff out there). So in my opinion in a research environment there are 2 kinds of activities: computational/programming stuff, where unix and free software have a clear advantage both on desktops and of course on HPC (of course it depends how it looks like in your domain AND in your research group), and on the other side wiriting documents and interacting with others (reports, proposals, data exchange, papers). You should have 100% control of the first category, but still have to factor in cooperation with colleagues (i.e.: if everyoen is working on matlab and you are supposed to extend and re-use their developments... probably you should too. At least try sci-lab and octave); but you can definitely compromise on the second. Cheers and good luck, domanov
Re: [O] General advice beyond Org
Just an update to let you know that I decided to migrate from Org-mode+LaTeX to ODF-and-related, particularly because of LPPL+GPL incompatibility, caused by LaTeX and related projects and because ODF-and-related are easier for the other people to participate and see the changes (no need to compile a .pdf nor to download 4 GiB of software). ODF 1.2 (which is used by default at least in LibreOffice 5) is good and offers many features similar to Org-mode, including adding files to each other, interacting with spreadsheets (look for "relative DDE link"), and also offers bibliography/reference manageemnt, along many other things. Although I do want to point out that you might want to go to View -> Disable "Show figures", so that LibreOffice Writer .odt documents are more editable and less slow. Also, note that you must recommend people to use LibreOffice to open the files. Microsoft says to have support, but it's not excellent. You may also want to import other .odt/.rtf/.doc/.docx files inside the main one. The tricks are that if you do so using "Insert" -> "Section" and tick "Link", the inserted section will use the main document's styles, not their own. Besides, for these files, since they *do* have notion of what is a "page break", then they will inevitably start in the next page. Also, inserting them this way may replace or add document metadata/properties (look in "File" -> "Properties"). at the same time, some files that you want to add are actually drawings made in LibreOffice Draw. In all the cases you might want to keep their own styling. To do this export them to .pdf. I use this: # Please close any running LibreOffice, or `soffice' silently fails. # No need to specify target file name. while read each_file do soffice --headless \ -convert-to pdf \ "${each_file}" done < "Figure"/"image", tick the box that has "Link" and select the image that you want to insert. Do this for each .png image. The "link" options are important so that the main document picks any change made to the .png image, otherwise LibreOffice will insert the entire image in the .odt, which will also make it more heavier to attach in e-mails (but requires the other person to also have the linked file in the same place). A caveat of the manual .png insertion is that if a .pdf happens to have more or less pages than the last conversion to .png, then you will need to add or delete the related links and their corresponding figures in the main .odt file. If someone has better solution please share. Additionally, one can't do "Insert" -> "OLE Object" to insert .odg or .ods files because these *cannot* break across pages, and don't look good when printing. This OLE feature wasn't made for printing purpose, but to facilitate editing without leaving the same program. If I recall correctly, it's a Microsoft kludge. As for tabular/table results produced by R, use and abuse of `write.csv'. Besides, make R output graphics to a .png image (use the `png' command/device). For all of this, write an .R/.r file and use Rscript to run it. The R-produced .png files can be inserted in the main .odt document I described earlier, no need to repeat the explanation. What you need to tweak in the `png' R command/device is the `pointsize' and `res' arguments. Something like this would do: ## The variables are here just for explanation. ## The standard DPI/`res' of the `png' command/device. R_img_dpi <- 72 ## The standard pointsize of the `png' command/device. R_pointsize <- 12 ## The new DPI/`res' of our image, to make things sharp. ## Just changing `width' or `height' isn't enough. sharp_img_dpi <- 90 png(file="Plot.png", height = 768, pointsize = R_pointsize * sharp_img_dpi / R_img_dpi, res = sharp_img_dpi, width = 1024) plot(something) ## ... or output some graphic. ## Close/save the .png image. dev.off() Now you ask, how to insert the .csv files in the main .odt document as tables in a dynamic way (such that if the .csv contents are changed by a external application, LibreOffice picks the modifocation)? To partially answer that question, I suggest you to make a new .ods spreadsheet set/document, and for each .csv, use "Spreadsheet" -> "Insert spreadsheet from file", select the .csv, enable/tick "Link", save the .ods. With that done, go to the spreadsheet/tab in LibreOffice Calc that you want to insert in your main .odt, click on the square between the column name A and which is above row name 1 (this will select the entire spreadsheet), copy (Ctrl + C), and Ctrl + Shift + V in the .odt, select "DDE link". To style the table, do it in the .odt document, not in the .ods spreadsheet. Particularly, if you want to make tables with consistent formating, make the first example tab
Re: [O] General advice beyond Org
For posterity: I have answered to the messages on this thread elsewhere. Thanks! - ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of the NSA's hands! $24.95 ONETIME Lifetime accounts with Privacy Features! 15GB disk! No bandwidth quotas! Commercial and Bulk Mail Options!
Re: [O] General advice beyond Org
As a student, you simply need to go along with your supervisor's recommendations. You are not in a position to dictate the terms. Using the proprietary tools will not hurt you, unless you need to buy your own. If it were the case that you needed to buy your own, then I would ask your supervisor for another solution. Even as a Junior faculty member, you may be in close collaboration with other faculty and should follow the consensus. That is how you work with other people effectively. You don't keep asserting that your solution is better. When you are calling the shots, you can use the tools you wish. So, you need to adjust your attitude. It may be that you are presenting the issue of principles - I prefer free, you prefer proprietary, but that is not really the true issue. Maybe you don't know the proprietary tools and don't want to learn them or feel you can't learn them. Choice of tools you use is no reason to switch graduate programs. This is entirely a matter of getting along with other people, not being selfish, etc. These are life skills we are talking about. Kevin Buchs On Thu, May 17, 2018 at 7:28 PM, wrote: > Hello, > > _I_ need help. I am in graduate school, and I keep having issues with my > advisor for my strong inclination to use free software. I am obviously not > in position to refuse, but she dislikes to have discussions about it. She > pays a stipend to me every month, and my tuition is waved. > > Is anyone here aware of a place where they do computational human > biomechanics, mechanics, materials or finite elements where I could > interact with free software? (having github, LaTeX, Python, etc.; avoid > Micro$oft products, Matlab, Mathematica, etc.). Is there no place where one > can simply use free software on a daily basis? > > It seems from her comments that I am, otherwise, a good researcher. She is > a nice person, but I fear that this may become an issue in the future for > me (whether with her or other people). > > As a student or junior faculty, how do you go about this? Do you just nod > and wave your freedom good bye? > > Thank you! (I will post this in other fora as well; don't let that to > discourage you from answering, please). > > - > > ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of > the NSA's hands! > $24.95 ONETIME Lifetime accounts with Privacy Features! 15GB disk! No > bandwidth quotas! > Commercial and Bulk Mail Options! >
Re: [O] General advice beyond Org
This is a super wise advice : >> Be a scout in the proprietary camp. Learn the tools your instructors are >> willing to teach. Learn what it takes to achieve the same results with free >> software. Learn the difference in workflows and user experience. Comparing stuff in scenarios you don't invent yourself is super enlightening. Once you don't define the scenario, all sorts of edge/unexpected situations arise. For example, if you work with math stuff, I'm sure you'll find interesting differences between computations results (e.g. matlab equations solving versus say Octave). stF > Le 18 mai 2018 à 12:54, Yuri Khan a écrit : > > > On Fri, May 18, 2018 at 7:29 AM wrote: > > > _I_ need help. I am in graduate school, and I keep having issues with my > > advisor for my strong inclination to use free software. I am obviously > > not in position to refuse, but she dislikes to have discussions about > > it. She pays a stipend to me every month, and my tuition is wa[i]ved. > > > Is anyone here aware of a place where they do computational human > > biomechanics, mechanics, materials or finite elements where I could > > interact with free software? (having github, LaTeX, Python, etc.; avoid > > Micro$oft products, Matlab, Mathematica, etc.). Is there no place where > > one can simply use free software on a daily basis? > > Are you required to pay for licenses for proprietary software you are asked > to use? Chances are, your school is getting academic discounts, and you get > to use it for no charge. > > Your instructors and professors probably have a lot of experience with > those tools. They are understandably reluctant to switch, because the tools > work well enough for them. > > Also, as a student, you do not have sufficient influence to convert > everybody at your school to free software. > > > As a student or junior faculty, how do you go about this? Do you just > > nod and wave your freedom good bye? > > The point of education is to get exposed to many tools, techniques and > workflows. By limiting yourself to free software only, you will miss out. > > Be a scout in the proprietary camp. Learn the tools your instructors are > willing to teach. Learn what it takes to achieve the same results with free > software. Learn the difference in workflows and user experience. > > You will find something you can do with free software that you don’t know > how to do with proprietary tools. Ask your teachers. They will either point > you at something you missed (and then you can study it); or they will admit > that feature is nice but their tool doesn’t have it (and then you have > demonstrated the merits of free software); or they will say it’s not > important. > > You will also likely find more than a few points where non-free software > delivers better UX. Use that knowledge to improve free software so that it > can compete with proprietary software on UX terms, not only on the issue of > freedom. >
Re: [O] General advice beyond Org
On Fri, May 18, 2018 at 7:29 AM wrote: > _I_ need help. I am in graduate school, and I keep having issues with my > advisor for my strong inclination to use free software. I am obviously > not in position to refuse, but she dislikes to have discussions about > it. She pays a stipend to me every month, and my tuition is wa[i]ved. > Is anyone here aware of a place where they do computational human > biomechanics, mechanics, materials or finite elements where I could > interact with free software? (having github, LaTeX, Python, etc.; avoid > Micro$oft products, Matlab, Mathematica, etc.). Is there no place where > one can simply use free software on a daily basis? Are you required to pay for licenses for proprietary software you are asked to use? Chances are, your school is getting academic discounts, and you get to use it for no charge. Your instructors and professors probably have a lot of experience with those tools. They are understandably reluctant to switch, because the tools work well enough for them. Also, as a student, you do not have sufficient influence to convert everybody at your school to free software. > As a student or junior faculty, how do you go about this? Do you just > nod and wave your freedom good bye? The point of education is to get exposed to many tools, techniques and workflows. By limiting yourself to free software only, you will miss out. Be a scout in the proprietary camp. Learn the tools your instructors are willing to teach. Learn what it takes to achieve the same results with free software. Learn the difference in workflows and user experience. You will find something you can do with free software that you don’t know how to do with proprietary tools. Ask your teachers. They will either point you at something you missed (and then you can study it); or they will admit that feature is nice but their tool doesn’t have it (and then you have demonstrated the merits of free software); or they will say it’s not important. You will also likely find more than a few points where non-free software delivers better UX. Use that knowledge to improve free software so that it can compete with proprietary software on UX terms, not only on the issue of freedom.
Re: [O] General advice beyond Org
Be aware that free software is politcally loaded. It's just not a matter of having the right or best tools, it' sometimes a question of ideal, that is something that is *very* hard to negociate about... Moreover, if the people you work with use, say Word, it's pretty tough to bring in, say Latex. Because you'll disrupt the organisation of the team. In the case of emacs, though, things are easier : it's made to work with text files and that is quite compatible with any other proprietary software. You won't affect anybody's job with that. Here at my job, I don't control any of the software I use (I have to use Oracle, Windows, Skype), but I can choose the software that *I* use for myself. So it's a balance. Changing other's mind, or methods is super hard, what you experience is just the normal. It'd be nice to know why your advisor rejects free software equivalents (lack of features ? fear of legal battles ? organisational ...) Stefan > Le 18 mai 2018 à 02:28, ed...@openmail.cc a écrit : > > > Hello, > > _I_ need help. I am in graduate school, and I keep having issues with my > advisor for my strong inclination to use free software. I am obviously > not in position to refuse, but she dislikes to have discussions about > it. She pays a stipend to me every month, and my tuition is waved. > > Is anyone here aware of a place where they do computational human > biomechanics, mechanics, materials or finite elements where I could > interact with free software? (having github, LaTeX, Python, etc.; avoid > Micro$oft products, Matlab, Mathematica, etc.). Is there no place where > one can simply use free software on a daily basis? > > It seems from her comments that I am, otherwise, a good researcher. She > is a nice person, but I fear that this may become an issue in the future > for me (whether with her or other people). > > As a student or junior faculty, how do you go about this? Do you just > nod and wave your freedom good bye? > > Thank you! (I will post this in other fora as well; don't let that to > discourage you from answering, please). > > - > > ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of the > NSA's hands! > $24.95 ONETIME Lifetime accounts with Privacy Features! > 15GB disk! No bandwidth quotas! > Commercial and Bulk Mail Options! >
Re: [O] General advice beyond Org
perhaps we can start thinking about improving registration between formats? if you export org [you posted to org mailng list] to a foreign format, you want your collaborator to be able to edit, save, send back without raising a sweat. now you have to integrate the changes. you want to do this without annoyance. suppose you export comments in the foreign format that contain the equivalent of persistent markers. you might or might not be willing to put org id or custom id on every heading, but there might be workarounds that are not so intrusive. maybe your source can contain comments with markers. dunno. if your exported document is a subtree within a huge org file that you edit all the time, registration allows your software to identify that subtree, so you're not trying to change anything outside that subtree. that alone is a win. but maybe we can do more. the markers can register sections or even paragraphs if you're doing intensive collaboration. the tricky part might be getting standard tools to understand that the mapping of markers takes precedence over everything else. details of this handwavey and possibly impossible brainstorm are left as an exercise for the reader.
Re: [O] General advice beyond Org
On 2018-05-18, at 15:50, hymie! wrote: > For example, good luck finding free software that will do your taxes. I, for that matter, do not use any proprietary software to do my taxes. (And BTW, I'm not religiously following the "only use free software" mantra, in fact, I feel some distance to the FSF ideals.) Best, -- Marcin Borkowski http://mbork.pl
Re: [O] General advice beyond Org
On 2018-05-18, at 21:57, Adonay Felipe Nogueira wrote: > c) better: do it with only free/libre software, and perhaps even teach >or show the people involved how to make use of tools that support >your workflow. For example Software Carpentry has awesome >collaborative material on the basics of VCS using Git and of >statistics wih R. > >If you don't have time to teach, make use of a tool that eases *them* >participating in their terms. > >As an example, I'm writing my final course work using Org-mode, LaTeX >and TikZ/PGF (this last one is for graphics), and whenever I want to >send a snapshot for review to my advisor I do so through making a >.pdf, but there is even more... > >The .pdf files don't actually track changes, so I must go into the >extra step of doing the following: Or use latexdiff (in case of LaTeX). Hth, -- Marcin Borkowski http://mbork.pl
Re: [O] General advice beyond Org
> It is only when we have to collaborate directly that the issue > arises. I guess that it's a similar situation as you are having > (programming? she does not care, I can do whatever I want; publication > abstract? she wants a DOCX or DOC). Collaborating on an article does require a fairly "deep" integration of various people's tools, so some compromise often need to be made. If she's used to using Word to edit documents, then it's likely going to be difficult to convince her to use something else, at least during your tenure as student. What I do usually in those cases is the following: - I refuse to install proprietary software, so in the worst case I'll edit a .docx document with LibreOffice (I don't see why she'd object to that under the imperfect compatibility between LibreOffice and Word gets in the way). [ BTW, If imperfect compatibility between LibreOffice and Word gets in the way, you might try and look for some other version of Word than hers, and find other incompatibilities (the various Word versions also suffer from imperfect compatibility), so as to show her that the issue is not just due to your use of Free Software. ] - You can try and get her to install the ODT plugin for Word so she can open ODT documents as well as .docx in her Word program. I often make the effort to only send ODT documents, even when it's a modification of a document that was sent to me in .docx format (on the premise that I shouldn't be the only one to bear the brunt of the format war). - Depending on how many changes/annotations she contributes to the document, you might be able to keep your original in your favorite format (LaTeX, Org, you name it); convert it to ODT or .docx before sending it to her; and then integrating her changes/annotations by hand into your original document. Using Git with ODT/.docx documents is about as pleasant as pulling teeth in my experience, so there's no point trying to convince her to try it out as long as she sticks to such WYSIWYG thingies. Of course, the real problems start when she wants to use some *really* poorly supported format like Apple's Pages. Stefan
Re: [O] General advice beyond Org
2018-05-18T00:28:22+ ed...@openmail.cc wrote: > Hello, > > _I_ need help. I am in graduate school, and I keep having issues with I'm undergraduating (seeking a bachelor's degree in organization management). :D > _I_ need help. I am in graduate school, and I keep having issues with > my advisor for my strong inclination to use free software. I am > obviously not in position to refuse, but she dislikes to have At first glance I would recommend you to keep using free/libre software only, and advocating for it where you live, work and study. But please read on... > discussions about it. She pays a stipend to me every month, and my > tuition is waved. ... Now this is a tricky challenge. Not that difficult, but as far as I can see these are the options: a) worst: make the compromise and use these non-free tools in your computer (the same applies when using a virtual machine or a container), because all-in-alll, it's still your personal computer. Besides, the virtual machine or container can misbehave and impact your real system or personal files. You will still have to deal with side-effects caused by loss of control over your own computing, let alone the need to learn how to use that non-free tool; b) somewhat better, although slow: use another computer (or get one from a rent) to do the work, and only do the work with that machine. The same case described in the second paragraph of (a) applies here; c) better: do it with only free/libre software, and perhaps even teach or show the people involved how to make use of tools that support your workflow. For example Software Carpentry has awesome collaborative material on the basics of VCS using Git and of statistics wih R. If you don't have time to teach, make use of a tool that eases *them* participating in their terms. As an example, I'm writing my final course work using Org-mode, LaTeX and TikZ/PGF (this last one is for graphics), and whenever I want to send a snapshot for review to my advisor I do so through making a .pdf, but there is even more... The .pdf files don't actually track changes, so I must go into the extra step of doing the following: --8<---cut here---start->8--- # # Convert old .pdf work snapshot to text. Makes a .txt file of the same # name, minus ".pdf". Caution here because if you don't specify a name or # path to place the .txt file, `pdftotext' will put it in the same # directory where the original is, contrary to what most commands do in # GNU+Linux. In Trisquel 8.0 Flidas, `pdftotext' comes from the # "poppler-utils" package. pdftotext "Documents/Work_---_2018-05-01.pdf" # Same for current .pdf which will be sent. pdftotext "Work.pdf" # Use GNU `diff' to produce Unified diff for text-only content. For us # who use GNU+Linux or GNU-with-Linux computers (GC) the diff files # commonly have .diff or .patch extensions, but we use .txt here so that # users of Windows computers (WC) can open those with ease in their # default plain text editor. diff -u "Work_---_2018-05-01.txt" "Work.txt" > "Work_diff.txt" # Among other unknown reasons, WCs make use of "\r\n" (carriage return # followed by line feed, commonly known as "CRLF" or "CR+LF") in the end # of each line to distinguish these plain text files from binary files. # WCs' default notepad will open a non-CRLF file but with all lines # joined, so we correct that using the `sed' line below. The side-effect # for us GC users is that some editing software might present two line # breaks. sed -i '/\r$/! { s/\($\)/\r\1/g }' "Work_diff.txt" --8<---cut here---end--->8--- Then send them both the .pdf and the diff file (the one which has .txt extension of course). And explain to them that the .txt is plain text that can be opened in plain text editor (usually called "Notepad" in Windows), and mention that it essentially shows the difference between old and new versions, and that: - Lines that begin with "+ " is new content; - ... "- " old content being removed; - ... "@@ -old_start,count_old +new_start,count_new @@" a line jump to given "old_start" line in the old file. With all that said, the advantages of .pdf files is that the advisors can highlight and annote/comment on these, save the changes and send it back to you (they can't change the structure or content of the document itself, but can at least give you hints). With all the options I presented, there is still another issue which is quite common at least in the college I study: the advisors don't actually orient people that well here, so even if someone theoretically decides to "suck it up and use non-free software anyways" this doesn't stop the advisor from being too vague as to give comments such as "it's not compliant with the institutional norms" (what exactly i
Re: [O] General advice beyond Org
Hi Edgar, 2018ko maiatzak 18an, -ek idatzi zuen: > It is only when we have to collaborate directly that the issue > arises. It sounds like the issue you are having is about collaboration workflow, and not about the usage of free software per se. Reading between the lines, it sounds like your biggest difficulty is with Microsoft Word. Itʼs very unlikely that you will be able to convince your advisor to switch to another program when writing with you. As Diego said, it is ultimately up to you whether you can live with this. But there are certainly compromises you could entertain that might make it easier. There are important benefits, to a field and to individual researchers, of open analyses. On the other hand, what maters about a scientific publication is principally the words themselves and where they are published – not the workflow that was used to create them, which mostly passes into irrelevance once they become part of the scientific record. So you might find pragmatic benefits to focusing on free software analysis tools and programming languages, and on the importance of publicly releasing analysis materials (whether based on free software or not) at an appropriate stage of the research, rather than on document authorship workflow where your advisor seems to have a particularly entrenched position. Another suggestion to reach out to other graduate students, who have the surplus of time* and lack of pre-established workflow habits conducive to learning new techniques. This wonʼt directly solve your issues with your advisor, but if you are contributing to the success of free software in other areas you might feel like your sacrifices with her are being balanced out. (*Having been a graduate student, Iʼm only too aware of the falsity of the premise that grad students have ample free time in an absolute sense. But relative to other career stages, grad students are probably the best situated in that regard. Itʼs also true that there are many things that grad students need to learn that could be learned either with free or nonfree software. The marginal time cost of replacing nonfree software in that learning with free software is likely to be small.) Itʼs also true that free software has network effects. Once someone is using R or Python, they are introduced to things like Jupyter or knitr (which are literate programming systems) – or even org mode. They also get exposed to VCS (like git), free text editors (like emacs, or RStudio), and other tools that do not directly replace Word but contribute to an alternate ecosystem. They might eventually be induced to switch their writing software of choice because of the features of such environments. So by evangelizing the pieces of free software that are most appetizing to others in your field, you are laying the groundwork for subsequent improvements that might initially be a harder sell. Finally, a very pragmatic suggestion. You might suggest to your advisor that you and her collaborate via Google Docs rather than MS Word. This is something I have found helpful with colleagues of mine who are not otherwise prepared to change their writing habits. The Google Docs interface is very similar to Word (but actually avoids some of the radical UI changes that MS has made recently, which might make it even more appetizing to certain users). While Gdocs is not free software (as itʼs important to point out), it enables me to use less proprietary software, on average. Iʼve never been able to get Libreoffice to work satisfactorily for iterative edits to a Word doc; I find that it too often loses formatting, included images, or otherwise doesnʼt interoperate with Word well enough. So in the absence of Google Docs I would have to maintain a Windows system on which to use Word. With Gdocs I have one browser tab that runs unfree JS, but the rest of my system is GNU/Linux. (There are also benefits to the online-first nature of Google Docs, which avoids the emailing back and forth of dueling versions of a Word document that I have sometimes encountered in groups that primarily use Word – but these are orthogonal to the free/nonfree distinction.) I hope that some of this comes as useful advice. -- Aaron Ecay
Re: [O] General advice beyond Org
In our last episode, the evil Dr. Lacto had captured our hero, ed...@openmail.cc , who said: > I am in graduate school, and I keep having issues with my > advisor for my strong inclination to use free software. [...] > > Is anyone here aware of a place where they do computational human > biomechanics, mechanics, materials or finite elements where I could > interact with free software? First question -- it sounds like you are doing very specific research with very specific tools, software, equations, and things like that. Are you sure that free software exists that will do what you want? For example, good luck finding free software that will do your taxes. > Do you just nod and wave your freedom good bye? Second question -- you keep using that word "free". Are you really "free" in this situation? You said you are getting tuition covered and a stipend. The way employment typically works is that, in return for salary and/or compensation, you give your full devotion to your employer's wants and needs instead of your own. Using your employer's software is not a huge jump. I don't mean this as a personal attack. That's how it works. I am "free" to wear a t-shirt that says "F**K THE POLICE" on it, but the person who pays my salary would prefer if, for 40 hours each week, I wear a different shirt. I am "free" to ignore his request. He is "free" to stop paying my salary. So I'm afraid that's my answer. Suck it up and do what the nice person who is giving you lots of money wants you to do, they way he/she wants you to do it. --hymie! http://lactose.homelinux.net/~hymiehy...@lactose.homelinux.net
Re: [O] General advice beyond Org
Hi Edgar, As in many other contexts, it’s important to keep the big picture in mind. As a grad student, is your goal to learn about your field, to do interesting work/research, and to eventually graduate? Or is it to defend your ideals and use the software you like? If it’s the second, by all means the software you use should be a central consideration (to the point of looking for other places of study, as suggested in your original post). But if it’s the first (as it should, IMO), then the central considerations change: is your professor good/nice/competent (insert your own criteria here)? Does she foster your work/research in productive ways? Does she give you good challenges and research topics? Only you can answer those questions. You can always compromise. Not all of us get to use only the tools we like all day long. In my case, I like my job very much, despite the fact that I have to use tools like Exchange, Sharepoint and Jira. But at home, during my free time, I get to code and use whatever tools I want (e.g. Emacs, org-mode, Elvish, Hammerspoon). I get to use some of them at work too, but I am aware that I have to stick to the accepted standards of communication and collaboration with others. From what you say, the tools your advisor uses are the recognized/accepted ones for doing the work. You could try to challenge this status quo, given enough time and energy. But again, think about what your goals are. You have to choose your battles. In any case, after you graduate, you can go on an be much more selective about (or even, define yourself) the tools with which you work. As a former grad student myself, I can give you two pieces of wisdom I received over the years, one from my Ph.D. advisor, and one from one of my colleagues. Both express the same feeling: “You may think now that getting your Ph.D. is the goal, but it’s only the beginning. The Ph.D. only opens the door for whatever you want to do next” “The goal of a Ph.D. is to finish it” All the best, —Diego > On 18 May 2018, at 10:10, ed...@openmail.cc wrote: > > On 2018-05-18 07:12, S. Champailler wrote: >> Be aware that free software is politcally loaded. It's just not a >> matter of having the right or best tools, it' sometimes a question of >> ideal, that is something that is *very* hard to negociate about... >> Moreover, if the people you work with use, say Word, it's pretty tough >> to bring in, say Latex. Because you'll disrupt the organisation of the >> team. >> In the case of emacs, though, things are easier : it's made to work >> with text files and that is quite compatible with any other >> proprietary software. You won't affect anybody's job with that. >> Here at my job, I don't control any of the software I use (I have to >> use Oracle, Windows, Skype), but I can choose the software that *I* >> use for myself. So it's a balance. >> Changing other's mind, or methods is super hard, what you experience >> is just the normal. It'd be nice to know why your advisor rejects free >> software equivalents (lack of features ? fear of legal battles ? >> organisational ...) >> Stefan > > Merci, Stefan. I have tried to understand her point, and I can dissect it > into: > > 1. She does not see the advantage of having to learn how to use anything > else. It works well for her, why change and waste time on doing it? > > 2. She likes and is used to the "features" of the software (today, I > discovered that one of these is the so-called "track changes"; I swear I have > tried to introduce her to Git, not that she cares). > > 3. I think that she is used to the interface. > > 4. She says (and I have no reason to question) that the whole department uses > the proprietary software that she uses. It is an imposition to others > (including her) to ask them to use something different. > > It is only when we have to collaborate directly that the issue arises. I > guess that it's a similar situation as you are having (programming? she does > not care, I can do whatever I want; publication abstract? she wants a DOCX or > DOC). What I find unfathomable is that I can produce the format that she > needs (even with style) with free software (thanks community!), but what I > perceive as her reluctance to my software (or just plain miscommunication) > prevents her from informing me or me understanding what exactly it is that > she considers important. In other words, she does not seem to want to deal > with it in any way. > > I'm sorry, I didn't want to make this very long. I hope that I explained > myself. > > The count goes like this (so that everyone knows that I am listening, the > count is by far the least important): > - Yield partially (1) :: You will have to work with proprietary software in > some way, but not always. > - There is no escape (1) :: You will have to work with proprietary software > > - > > ONLY AT VFEmail! - Use our Metadata Mitigator
Re: [O] General advice beyond Org
On 2018-05-18 07:12, S. Champailler wrote: Be aware that free software is politcally loaded. It's just not a matter of having the right or best tools, it' sometimes a question of ideal, that is something that is *very* hard to negociate about... Moreover, if the people you work with use, say Word, it's pretty tough to bring in, say Latex. Because you'll disrupt the organisation of the team. In the case of emacs, though, things are easier : it's made to work with text files and that is quite compatible with any other proprietary software. You won't affect anybody's job with that. Here at my job, I don't control any of the software I use (I have to use Oracle, Windows, Skype), but I can choose the software that *I* use for myself. So it's a balance. Changing other's mind, or methods is super hard, what you experience is just the normal. It'd be nice to know why your advisor rejects free software equivalents (lack of features ? fear of legal battles ? organisational ...) Stefan Merci, Stefan. I have tried to understand her point, and I can dissect it into: 1. She does not see the advantage of having to learn how to use anything else. It works well for her, why change and waste time on doing it? 2. She likes and is used to the "features" of the software (today, I discovered that one of these is the so-called "track changes"; I swear I have tried to introduce her to Git, not that she cares). 3. I think that she is used to the interface. 4. She says (and I have no reason to question) that the whole department uses the proprietary software that she uses. It is an imposition to others (including her) to ask them to use something different. It is only when we have to collaborate directly that the issue arises. I guess that it's a similar situation as you are having (programming? she does not care, I can do whatever I want; publication abstract? she wants a DOCX or DOC). What I find unfathomable is that I can produce the format that she needs (even with style) with free software (thanks community!), but what I perceive as her reluctance to my software (or just plain miscommunication) prevents her from informing me or me understanding what exactly it is that she considers important. In other words, she does not seem to want to deal with it in any way. I'm sorry, I didn't want to make this very long. I hope that I explained myself. The count goes like this (so that everyone knows that I am listening, the count is by far the least important): - Yield partially (1) :: You will have to work with proprietary software in some way, but not always. - There is no escape (1) :: You will have to work with proprietary software - ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of the NSA's hands! $24.95 ONETIME Lifetime accounts with Privacy Features! 15GB disk! No bandwidth quotas! Commercial and Bulk Mail Options!
Re: [O] General advice beyond Org
On Thu, 17 May 2018 20:28:22 -0400, wrote: Hello, _I_ need help. I am in graduate school, and I keep having issues with my advisor for my strong inclination to use free software. I am obviously not in position to refuse, but she dislikes to have discussions about it. She pays a stipend to me every month, and my tuition is waved. Is anyone here aware of a place where they do computational human biomechanics, mechanics, materials or finite elements where I could interact with free software? (having github, LaTeX, Python, etc.; avoid Micro$oft products, Matlab, Mathematica, etc.). Is there no place where one can simply use free software on a daily basis? It seems from her comments that I am, otherwise, a good researcher. She is a nice person, but I fear that this may become an issue in the future for me (whether with her or other people). As a student or junior faculty, how do you go about this? Do you just nod and wave your freedom good bye? Thank you! (I will post this in other fora as well; don't let that to discourage you from answering, please). What is your field? In some areas of research the foremost software tools have been developed on a MS platform and there is no escape unless you go and develop your own tools. Allow me to illustrate from a non-software perspective, in two different directions. I happen to own a substantial number of horses, and thus find myself employing the services of a farrier. That's the person who trims the hooves and fits shoes. My previous farrier, now retired, made some of his own tools and avoided using the top, well-known brand, GE. (It's GE Forge & Tools, NOT General Electric!) "Too expensive," he said. "Not worth all that extra money." My current farrier works three times as fast as the other guy, and uses nothing but GE tools. Clearly, he can fit in perhaps twice the number of customers a day, and the tools pay for themselves. He could make his own, as can anyone who owns a forge, an anvil, and hammers, but why bother? He makes perhaps $300 an hour when working on horses, and nearly nothing when trying to build tools. I also get questions from young folks between the ages of 8 and 16 who love horses, and want a career working with horses. They hope for a job where they will clean stalls and exercise horses, and maybe help with training. My suggestion to them is to find a profession such as accounting or medicine where they will be able to make enough money to own several horses. After a day cleaning stalls and brushing horses at minimum wage or less, who wants to saddle up Yet Another Horse and go riding? The accountant who can fathom the intricacies of expenses for a Thoroughbred race stable will be well rewarded, and may even get invited to ride. These words are rather far afield from your actual question, but I think you do need to reflect carefully on where your interests actually lie. So back to free software itself. Read, if you have not already done so, this article by rms: https://www.gnu.org/philosophy/open-source-misses-the-point.en.html . Then ponder whether you want your career to follow his delightfully weird footsteps, or whether your field requires a totally different approach. I'm sure that rms would disagree with me--he has every time I've spoken with him--but his is not the only philosophy available.
[O] General advice beyond Org
Hello, _I_ need help. I am in graduate school, and I keep having issues with my advisor for my strong inclination to use free software. I am obviously not in position to refuse, but she dislikes to have discussions about it. She pays a stipend to me every month, and my tuition is waved. Is anyone here aware of a place where they do computational human biomechanics, mechanics, materials or finite elements where I could interact with free software? (having github, LaTeX, Python, etc.; avoid Micro$oft products, Matlab, Mathematica, etc.). Is there no place where one can simply use free software on a daily basis? It seems from her comments that I am, otherwise, a good researcher. She is a nice person, but I fear that this may become an issue in the future for me (whether with her or other people). As a student or junior faculty, how do you go about this? Do you just nod and wave your freedom good bye? Thank you! (I will post this in other fora as well; don't let that to discourage you from answering, please). - ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out of the NSA's hands! $24.95 ONETIME Lifetime accounts with Privacy Features! 15GB disk! No bandwidth quotas! Commercial and Bulk Mail Options!