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What does "Application review begins ..." practically mean in job ads in computer science in USA?
As opposed to Do they really mean "in all areas" and "will continue to be accepted until..." in Computer Science faculty opening ads in the US? , we sometimes even see a softer language without a final deadline in faculty opening announcements:

Application review begins Date Y.

No final deadline ("until...") is given. How long after Date Y can one apply in the typical case?
(An aside: Assume that the applicant cannot get this information directly by asking, e.g., due to the absense of contact data, and that the applicants network, including that of the supporting advisors if there are any, does not cover the location.)
This question seeks answers from folks who have participated in search committees, have supervised them, or have received feedback as applicants. If it is the case for you, say so.

Both your questions boil down to one simple answer : get off your butt and get the application finished and submitted...

@SolarMike Already done, but there are, perhaps, 50 similar ones to go: either with a past deadline or a slightly different subdiscipline...

If they are interesting and not ancient then it may be worth applying : if they are "open" but 5 years back then probably not...

@SolarMike All are from this fall, i.e., the review-begin dates are 1 week till 3 months back.

It means that, shortly after date Y, the committee in charge of reviewing applicants will meet and discuss the applications that have been received up to that point and, if they like some of the candidates, they will be invited for interviews and, depending on how it goes, may get an offer. They committee may revisit the applicant pool at a later date and, if the position is still open, they may consider further applicants. So, in principle, you can apply whenever you want but if you wait until after date Y, you may miss out. Of course, it can happen that all good candidates are late but you shouldn't count on that.

In short, get your application in by date Y, or it might simply be ignored.  In all the searches I've been involved in with this kind of advertisementI've never seen a case where the committee did go back to look at later applications.

@BrianBorchers Thank you! Might I perhaps ask you to reveal in how many searches you have participated?

Thank you! When is "shortly after date Y" in your experience?

Somewhere between ten and 20 over the last 25 years.  Most in my own department, but several in other departments at my institution.   "Shortly afterward" can mean that the applications received by that date are reviewed and anything that comes in late is held in case the committee decides to go back.

... and anything that comes in late is held in case the committee decides to go back. - which it has never done in your experience, right?


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Do they really mean "in all areas" and "will continue to be accepted until..." in Computer Science faculty opening ads in the US?
The following is an extension of the question Job applications reviewed "until the position is filled" (i.e. soft deadline): What does that really mean?.
In most US job announcements of faculty openings (of any rank) in computer science I've seen no hard deadlines for applications and no hard subdiscipline designations. (In Europe, this is different: the deadlines and the subdiciplines are typically hard restictions.) Most of the time, we see sentences such as

The search will focus on candidates in the areas X1, X2, and X3. However, outstanding candidates in all research areas will be considered.

and

Preference will be given to applications submitted before Date Y, but we will continue accepting applications until the positions are filled.

Wee see such phrases way too often and may consider them boilerplate in the meantime.

Does the search team actually sometimes look at applications outside of the mentioned areas (X1, X2, and X3) and at the applications submitted after the deadline? Or are the above phrases introduced for some other reasons (legal, politics, ...), and the search team never looks at anything beyond the mentioned subdisciplines or anything past the deadline?
Has anyone already been hired despite being outside of areas X1-X3 or beyond the date Y?
In practical terms, if the applicant is a normal scientist but has missed the deadline, how long after that he/she should apply?
In practical terms, if the applicant is a normal scientist, is on time, but the subdiscipline is slightly off, should he/she still apply?
In practical terms, if the applicant is a normal scientist but the subdiscipline is slightly off and the deadline has passed, how long after that he/she should apply?

(An aside: Assume that the applicant cannot get this information directly by asking, e.g., due to the absense of contact data, and that the applicants network, including that of the supporting advisors if there are any, does not cover the location.)
This question seeks answers from folks who have participated in search committees, have supervised their work, or have received feedback as applicants. If it is the case for you, say so.

Only the search committee could answer your question. That being said, if I was interested in that position, I would apply.

@RichardErickson When I asked a search committee some question, it often resulted in no answer or in a very late answer...

This is an area where networking can stand you in good stead.  A feeler sent out to someone you know in that department can be helpful, to find out how far afield they'd be willing to go, and how far along they are in the process.

@aparente001 Sure. I'll add a sentence on that.

If the applicant's network doesn't cover this location, well, if you have chutzpah you could try this: the advisor, or a senior colleague of the advisor, calls someone high up at the place where the candidate is applying, to have an informal chat.  The person making the call could say that he has two or three excellent students who are job-hunting, and he'd like to get more information about the spot they're trying to fill, to figure out which student would be a good match.  If they are already too far along in the process to make an application worthwhile, the dean will probably say so.

@aparente001 Definitely. I've already thought of that. I'll add a sentece. Think of the case when there are no supportive advisors. One example is bad relationship with the formal boss, another is the associate/full professor case.

@LeonMeier - Oh my god this is getting complicated.  Like Calvinball if you've ever read Calvin and Hobbes.  Maybe you should write a new question.

@aparente001 I've simplified the corresponding para.

The job market is soo competitive you should apply to anything and everything, and tailor each application to the specific announcement.  // I don't understand your concern with boilerplate language.

As to the research area, whether they really mean that any research area will be considered is impossible to know from the ad.  Sometimes the search committee really is open to a broad range of areas; other times, there is really so strong a preference for one particular area that people from outside area have essentially no chance.  I have served on search committees of both types; although the relevant verbiage in the ad was the same in either case, in one case, a majority of the committee was committed to hiring somebody from a very narrow area.
As to the deadline statement, I think that is pretty much always meant seriously.  The statements is there so that the committee does not have any possible obligation to not consider applications that are not completed until after the deadline.  There's no practical reason for the committee not to consider applications that come in a little late, and in my experience, slightly late applications have always been given full consideration.
By "slightly late," I mean a couple weeks. Actual review of the applications by the committee typically doesn't start until that long after the due date. (That's particularly true if the due date is early, falling during the winter break or earlier.) The latest application that I can recall getting full consideration was completed about a month late, but at that point things are probably getting dicey. And (just like in graduate admissions) committee members are likely to be more flexible about the dates of recommendation letters than the package put together by the job applicant.

By "slightly late," I mean a couple weeks. — Having chaired an “all areas / preferred if by [date]” hiring committe in CS, I have to strongly disagree. I have seen successful applications submitted three months after the soft deadline in the ad. The only way to know if your application will still be considered after the deadline has passed is to ask. (And I have never seen any committee member look at the dates on the letters.)

@Deduplicator - I took Buzz to mean: There's no practical reason for the committee to disregard applications that come in a little late,

It makes sense to approach this question by thinking of the job ad as a contract. The department is making certain promises about the way the search will be conducted. For both legal and ethical reasons, you should interpret those promises in the most literal way possible: every word that is included matters and is included for a reason, and every word that is not included is also not included for a reason. Your prospects of being able to second-guess some sort of hidden meaning behind those words are therefore not very good: if the department wanted to let you know its precise intentions, it would have already done so by including that information in the job ad. None of us reading the ad from the outside can know any more than you do.
To put what I said above into practice, let’s see what the ad actually said and what we can read into it:

outstanding candidates in all research areas will be considered

Well, it means exactly what it says: the department will consider all outstanding candidates. If you apply and your area is not exactly what they said, and if you are outstanding, they will at least consider you. There are obvious advantages to the department leaving such options open for itself. For example, if a Turing Prize winner or some other famous computer scientist applies and they are not in the desired areas, the department may still prefer to hire them.
What if a normal computer scientist applies? Well, normal people can still be outstanding. We can’t say if you should apply, and can’t give any insight about what the department considers outstanding or why they inserted that language into the job ad. But it doesn’t necessarily have anything to do with legalities or politics - it could simply make good sense as a recruiting strategy.

Preference will be given to applications submitted before Date Y, but we will continue accepting applications until the positions are filled.

Again, this means exactly what it says: the department will continue to accept applications. If the reincarnation of Alan Turing applied three months after date Y and the position is unfilled, you can rest assured that there is a good chance they will be hired. And as for a normal, non-famous person, again none of us can say what your chances are if you apply two weeks, or one month, or three months, after the deadline. It depends how attractive you look compared to other candidates currently being considered.
As others have said, from a practical point of view the best thing is to apply and hope for the best. Good luck!

Thanks Dan. My fear was that the phrases as above looked way too boilerplate to me. (Similar to "women/veterans/... are preferred".) You have cleared these fears. Still, if you compare it to Europe, you get zero days behind the deadline there by default. As for "...none of us can say...", this is not quite right: people on search committees can speak about their experiences.

@LeonMeier I’m not sure I understand the distinction you’re making between boilerplate and non-boilerplate language. My answer applies to anything that’s written in a job ad, whether boilerplate or not, including the example in your comment.

That's not quite true. The world is full of biases, and adding a boilerplate para about preferring minorities does not increase their chances: more than simply adding text to the job ad is needed (and sometimes done). So, as for the minorities para, not all institutions really stick to their promise. My question is about the para about deadlines and subdisciplines, which also seems boilerplate enough to me.

@LeonMeier I never said that institutions always mean what they say, and I agree with you that’s not the case. My claim is more subtle: it’s that as a job candidate you gain no advantage by considering the possibility that they may not mean what they say. Take everything at face value is my advice, at least for the purpose of deciding on your actions. And I stand behind “none of us can say”. FWIW, I never served on a search committee but oversaw several searches as a department chair where I was in charge of  writing job ads (among other things) and worked closely with the search committee.

I think the way to think of it is that these statements exist so that applicants who don't fit the obvious stereotype of a candidate should not be discouraged from trying. You might have some disinguishing feature that makes up for the fact that you've worked outside the particular research area.

I'm a department chair (in physics, not CS) and have been involved in multiple searches.  The job market is very competitive (for you, the applicant), but second-tier schools are ALSO very interested in getting the best people we can get.  We absolutely prefer the areas we listed in the job advert, but we would be fools to reject an application from someone outstanding, and we leave you to define that; we'll know it when we see it.
(Also, discipline boundaries are fluid.  You might not be in area X1, but you might make a case in your application letter that X4 (your area) is very similar to X1.  Smart search committees know that they can get too focused and that what they really need might NOT be what they asked for)
As far as being late goes, I agree with the other answers.  The search committee often takes a couple weeks to have a meeting, and if you are under a month late and you ARE in a desired area, then we definitely want to see your app, because we may have gotten a lot of speculative apps from folks who are NOT in the prescribed area.  So yes, it feels tough to you, but search committees also worry.  A ''failed search'' (where you didn't find an applicant who fits, or your top choices turned you down) is a nightmare for a department.
Finally, as far as "chutzpah" goes ... we expect it in our applicants.  Definitely don't be too chicken to call up and ask, even if it's a cold call.  Harvard/Stanford/Berkeley can turn up their noses at you, but smaller schools will take your call.  It can't hurt you to try to get more info.  That's good advice for ANY job-hunting situation.

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Topics for consideration for someone interested in graduate school
What are some topics or questions that undergraduates or post-baccalaureates would have when they are considering applying to graduate school, particularly in the fields of biology, ecology, natural resources, or related fields in the US or Canada? Are there any publications, websites, blogs, or other resources that provide valuable discussions of such topics or at least a list of possible considerations? I have encountered many examples of resources for individual, specific considerations (e.g., how to apply for a particular fellowship), but I am looking for a more comprehensive inventory of topics, or better yet a general how-to guide.

This question is radically different from the original, which was not, IMO, a shopping question.

@Buffy is it more of a shopping question now? I read about shopping questions but also couldn't figure out how the previous one was a shopping question. I tried to reword it to make it clearer (from how I understood it) but did not mean to make it into a new question.

@selene, look at the difference with the first version. It is now asking for lists of external resources, not suggestions for a workshop. Clearly shopping now. I note that you weren't the first to alter it, of course. But you emphasized the shopping aspect.

@Buffy I see now where I can see the original one...I only saw this after the first set of edits. Thanks for clarifying!

Sorry for any confusion this question and the editing has caused. This was my first attempt writing a question for Stack Exchange and I've been unsure how to handle the possible shopping issue my original post had or if the subsequent edits have been helping or hurting. I appreciate any help trying to sort this out, though I also understand if this question is still better left closed.

Note that this answer was given for an earlier version of the question that asked for topics to cover in a workshop for undergraduates. The question is now very different. It wasn't originally a shopping question.

I have a few suggestions, but not a comprehensive answer. And it is broader than biology.
First, see the answer for the US to this canonical question about doctoral admissions. Note that it doesn't work the same for masters degrees.
In addition to the admissions process, make sure students know they maximize their chances of admission if they cast a broad net, in particular, not focusing only on a small set of "top" schools.
Second, if you want to include Canada, make sure you understand that there are differences and what they are.
Spend some time on explaining, not just the application issues, but the main requirements of obtaining a degree such as (in US) the early advanced coursework, preliminary/comprehensive exams, when to choose a professor and a topic and what to expect to have to do for successful research.
In the above, talk about the funding possibilities such as TA and RA and the time and effort that is required for that.
In the modern age you might have to talk about the progression from doctoral study to a suitable position, including postdocs and such. It isn't trivial.
You might even want to bring up the possibility of such things as burnout and how to find help for that if/when it happens.

And if you do thoroughly understand the Canadian system, please consider adding an answer for Canada to that canonical question.

Thank you for your suggestions! As to your point about US vs. Canada systems, I collaborate with several Canadian researchers from two Canadian universities and I applied to multiple Canadian graduate programs while looking for a grad position. While I do not have as in-depth an understanding of their system as the US, I feel I can at least speak to some of their similarities and differences to the level of a more introductory workshop and particularly for US-based students (that would be my audience) looking to apply to Canadian schools.

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I am a PhD student. How can I find collaborators that I can contribute work to and become a coauthor on papers?
I'm a PhD student almost completely on my own at my university.  I'm in my third year and its occurred to me I have had to drive every project forward almost entirely on my own.  I am the only student working on my topic in the world (I am working on a new remote sensing technique invented and patented by my supervisor).  However, because of this I have no one to get advice from and work with apart from my supervisor.  I am envious of others in my department (astrophysics) who get to collaborate together and gain far more support and papers.  I have had to push forward all of my papers (two first author) largely on my own.  I am keen to become a co-author on other work but I'm not sure how I join existing projects.  Does anyone have similar experience?  Could I just cold email scientists who might be working on projects I could contribute to?  I'm really struggling and alone

Why are you keen on becoming a co-author in the first place? What does that get you?

I suppose just increasing number of papers with my name on it.  My colleagues have a large number of papers to their name with comparatively less effort (i.e. they don't lead the study and do the majority of the work).

As a PhD student your job is to get your PhD. Now it will depend on where you are and their requirements, but multiple first-author papers is good. Sure, one or two papers with others to show either your flexibility or an application of your technique to other problems might be good. But get your degree above collecting papers...

I suspect that cold emailing will be entirely unfruitful. The way to start collaborations is to meet people and discuss ideas with them. Professional meetings are a good, maybe the best, way to do this, but you can't just passively attend them.
Other things that might be possible for some people is to have the university invite outside speakers who spend a couple of days interacting with graduate students and faculty. Or, one might be able to arrange a short visit elsewhere, give a talk, and spend a day or two interacting.
You probably need to finish your degree first, but make it a goal to meet and interact with people and to have those topical conversations with them.
I'll note that in some fields it is completely natural to interact as a student with only your advisor. Other faculty members probably have different interests than yours (and your advisors).
Make travel/conference support one of the things you look for in employment. Make departments with faculty that have similar interests a priority in job search. In some university departments, the coffee lounge is the most important room for idea development and exchange.
Over time, one can develop a circle of collaborators, but it won't be overnight and it is unlikely to get started with cold emails.
If all else is closed, it might be possible to have your advisor send emails to people in their circle, introducing you and suggesting you have something to offer. An email from a colleague is likely to be answered and requests more likely to be honored than any cold email from a student.

Thank you for your message.  I am hoping to attend a couple of conferences this year and make visits to universities.  Is it normal for academic careers to sometimes take more time to get going?  I'm just worried that I'm falling behind my colleagues who collaborate together extremely frequently whereas I have been a bit more of a one man band.

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My PhD supervisor gave up on me
I'm a 4th year PhD student in Germany. I started my PhD in a fully funded project and the funding will run out by next month. I'm still not close to finishing my PhD but I believe that I can finish it. But my supervisor has given up on me and this is bothering me. My PhD research is multidisciplinary and for that I had to learn some new technical skills too (as my second supervisor is from different discipline) which took a lot of time. At personal level I had been dealing with a lot of self-doubts and insecurities which also took a lot of time for me to recover and feel good enough to have the confidence to continue. The whole time I tried to do everything together to make my supervisors happy but in the process I lost my own voice in my own research. And now my first supervisor, who I am mostly with, has lost hope in me as I haven't been able to publish anything. In her way, she tried to help me but my own lack of trust on me took over most of the time. So now I am asking here if anyone has any advice to deal with these situations? For now I'll focus on completing the paper that I have been writing for one year now. Maybe that could help.

Can you elaborate on what it means that your supervisor has "lost hope in you"?

Lost hope in the sense that she doesn't think that I'll finish and I just found out about it. She never says anything directly but talked to one of the postdoc and others from my research group.

https://academia.stackexchange.com/questions/46250/how-to-deal-with-failing-a-student It's not the same situation, but you might be interested in what it looks like from the other end.

How much experience does she have with supervision? Also, how focused on her own career is she as opposed to focus on her doctoral students? I once had problems with these issues.

I worry you are making assumptions about her "giving up on you" from what you write. Unless she has told you that explicitly, you need to have a serious conversation with her.

How close are you to finishing the paper? Writing for 1 year seems excessive, but if you mean the whole process including experiments and analysis it looks more reasonable.
Also, what do you mean by "lost own voice in research"?

@Buffy: She might have given up in the sense that she genuinely believes her student won't finish and she might be planning for that. I have never met anyone supervising PhD students with a 100% graduation rate, no matter how willing both supervisor and student were.

"At personal level I had been dealing with a lot of self-doubts and insecurities which also took a lot of time for me to recover and feel good enough to have the confidence to continue" what does this mean?

4th year with no publications is actually a reason for your supervisor to lose hope. Unfortunately, it is the dark side of the academia. Publish or perish. She probably wants to spend the funding on a student whom she believes can publish at least a couple of papers in four years. I neither approve nor glorify this principle, but I can understand it.

Never mind what your supervisor's opinion is, (that doesn't matter a jot) what _ effects _ are you seeing/suffering?

I see mental health issue. You should seek help from university resources. Research is doable and your professor is qualified to guide you. Every professor wants their students to complete their degree and move on. So unless you are absolutely incapable professors won’t give up but they may slow down. Talk to your advisor and try to find a doable pathway.

First, it sounds like you are operating on second-hand information, which is tenuous.  Second, assume your advisor did say "I don't think X will finish."  This does not mean she has "given up" on you.  She may have recognized how you are struggling and, based on previous students, recognize that you are falling into the same pattern as others that did not finish.  This does not mean she has given up.  The real question is this: What is she doing to encourage your success?  What are YOU doing to assure your success?  Talking with her directly may be a great start.

@padawan Publication rate is discipline dependent and not a good blanket metric for a PhD student's productivity.

I was also a lost cause for the first 3 years, but then I worked my ass of in the fourth year and finally did it. I hope this gives you some hope!

@tnknepp Are there disciplines for which 4 years without publication is pretty normal? I'm not aware of any

@padawan While "normal" is a stretch, I know some subfields of physics where phd students spend the first few years building & tweaking their experimental setup, doing as many finicky measurements as possible and then writing everything up in a mad dash at the end. Add in some covid lockdowns, time for a few manuscript rejections and it's looking realistic (if unfortunate).

I'm sorry that you're in this situation. Since you're in Germany specifically, I think there might be some resources from your university or institute for this situation, which is why I'm advising a slightly different tack from WhatTheDuck.

Step 1: Plan for your basic needs

From what you're written, it seems unlikely that you will be able to graduate before your funding runs out. Based on your current position, do you qualify for unemployment money? Does your institute offer graduating stipends ("Abschlussstipendium") for students who go over time? If your institution has some sort of overarching structure for doctoral students (like a "Graduiertenkolleg"), can you ask a responsible person there what they've done for such cases? Is there an active Fachschaft or student union of sorts that can help you navigate the bureaucracy of applying for any financial aid you might qualify for? In a worst case (e.g. you will still need much more time than you have funding for), are there part-time jobs that could keep you afloat while you write up? You are not the first person to go over time on a PhD, and there's no reason to be ashamed of this. The goal of step 1 is to get a feeling for your remaining timeframe, and take off some of the pressure of your funding running out.

Step 1b: Mental Health

If you need professional support, now is a great time to go for help. Coaching might be a good option. It's also a good time to reach out to friends and family: talking to people who (presumably) couldn't care less if you finish in 4 or 5 years can be very grounding.

Step 2: Figure out the bare minimum

What are the bare minimum formal requirements to graduation at your institution? Assuming a worst case scenario, what is the absolute floor to achieving graduation? Figure out the preliminary answer in your (and potentially the Fachschaft/student representatives) estimation- presumably something along the lines of "some amount of science, a document of >x pages in format y, z referee suggestions". Does publishing the paper affect this? (e.g. by letting you defend cumulatively with a shorter thesis?) In an ideal world, what would you still want to do to wrap up your project? The goal of step 2 is to have some rough mental vision of how much work you still need to wrangle.

Step 2b: Paperwork is not the enemy

If you were employed in Germany, you presumably should have had some sort of annual progress meeting (Jahresgespräch). Do you have minutes/notes on those meetings? Did you write some sort of project agreement at the start of your PhD? Try to collect all of these things and reread them to get a feeling for the intended scientific scope. The progress meetings in particular should have included some sort of "this is where we are/how you're doing, this is where we're going" bit- how have those turned out. This is not about beating yourself up for falling short, but about getting an overview of the scope. (If you struggle negativity during this, ask a friend to go through them with you). If there were things you worked on that fell short of publication, are they still sufficiently well-documented to be written up for the thesis?

Step 3a (optional): Talk to supervisor #2

You mentioned that your project is multidisciplinary, and that you learned new technical skills for supervisor #2. How much credit can you get for what you've done in their discipline, and how much more would they want you to do to graduate? The placement of this step depends a bit on your relationship with them. If you think they might be a good resource to help you wrap up your project, it's a good idea to rope them in early. If you think this will cause more confusion (their expectations are too far away from supervisor #1's), you can skip them until Step 5.

Step 3b: Miscellaneous support

Ask everyone and anyone (other PhD students, admins, your doctoral program) about PhD-graduation support options. Is there a thesis writing club? Graduating stipends? Subsidised coaching? You are not the first or only one to struggle at the end of their PhD, and having an overview of what's available can help. Communication of German administrative structures is not always the best, and sometimes asking around is the only way to figure these things out. You don't need to go into detail to ask around, just; "oops, my project is going a bit over time, what help can I get to fix this"?

Step 4: Get supervisor #1 on board

Set a meeting with them to discuss your timeline to graduation. WhatTheDuck has already written about this, so I will be brief. The previous steps were about you figuring out what kind of financial (stipends, social security), professional (institutional staff, union, supervisor #2), social (your friends & family) and personal (your existing science) resources you can bring to the table. This can give you a bit of a framework for the discussion, and show that you're serious about finishing your project. Maybe you supervisor can help you with funding, but even if not, the main goal here is to agree on a timeline and scope for your remaining project.
It will probably feel difficult, but ideally try to keep this discussion on pragmatic, actionable tasks and timelines as much as possible. It would be nice if they believe in you, but what you need from them is an agreement of what should be in Chapter n. Make sure you write down your plans, then set a next meeting (with action points for what you need to do by then).

Step 5: Follow the plan

Assuming you get something workable out of Step 4, try to put aside your doubts and follow that agreement. If you struggle with doubts, go to Step 1b or Step 3b. You can also use Step 3a (talking to supervisor #2) if they're helpful, although I would absolutely stick to whatever you agreed on in Step 4.

Step 6: Disengage from the gossip train

Circling back to the start, I'm sorry that you're in this situation. Maybe your supervisor did express some cynicism to a postdoc, maybe they're stirring the pot. Either way, at the moment you only stand to lose by engaging with the gossip mill. It's deriving a wedge between you and your supervisor, and making you feel isolated. Once you've concluded Step 4, announce something vaguely optimistic to the gossip circle and then let them move onto other things- focus your in-office energy on your thesis, and your social energy on your friends, family and hobbies.
Edit: Upon re-reading, I'd also like to add that Steps 1-3 before the conversation are not about presuming any lack of faith from the supervisor, but about trying to be more agentive and independent as a (hopefully) soon-to-be-graduating student.

"If you were employed in Germany, you presumably should have had some sort of annual progress meeting (Jahresgespräch)." While I hope this isn’t the case here, in my experience these often are skipped in academia especially if the employee isn’t aware they can demand those - i.e. for students who focus on other concerns.

@MisterMiyagi Sadly I have to agree with you, but I thought it might be worth mentioning.

Sounds like you're having a tough time, and I hope it gets better for you.
The most important thing you need to do right now is take care of your mental health - whether that's by beginning (or continuing) counseling/therapy, etc. The "lack of trust" you mention (I'm unclear from the phrasing whether that's you lack trust in your advisor or in yourself) has clearly negatively impacted your program of study, and that is something counseling/therapy can help address. There is a tendency for Ph.D. students to go through cycles of mentally "doing better" before cycling back to mentally "doing worse." I encourage you, even if you think you're doing better, to get help now (if you haven't already), because it's a lot harder to reach out and get that help during those "doing worse" swings.
The second most important thing you need to do right now is communicate with your advisor. I know this sounds odd based on the issue you're having, but you need to sit down and have a talk with your advisor about what, EXACTLY, you need to accomplish in order to graduate, and come up with a plan, including timelines, of how you will go about accomplishing these things. Bear in mind that since the funding is about to run out, it is possible that your advisor simply doesn't have the money for you to finish - and this is something that you need to talk about with them, as well.
Having a concrete plan in place, and showing the initiative to put in motion a plan to finish, will probably be more helpful than anything else in convincing your advisor that you can finish.
Finishing the paper is a good start, but if you've been working on it for over a year now I think it's likely you need input from your advisor or someone else with more experience on what to focus on to finish that paper, so again - communication is important.

I am so sorry you are going through this.
I am starting a 5th year and can relate with most of your experience. For the entirety of my 4th year I believed my supervisor had given up on me (it didn't help him saying at some point that he tried to help me with task/time management recurrently but since I couldn't change my poor work habits he might just give up trying) and this brought about a new layer of imposter syndrome, frustration and anxiety/depression. Because this was someone I had taken as a scientific role model, the feeling of letting him down took a heavy toll on my mental health.
I can only share my experience going through similar situations so that you realize that at least you are not alone.
I believe your supervisor may be conflict avoidant and career oriented, like mine. If this is the case, there is no point insisting you need her help. They will expect you pick yourself up and self motivate to chase a question like they do, unaware it doesn't work the same for all people.
If I can give you a piece of advice is to worry less about what your supervisor thinks of you and work on building that self-trust. You reached this point in your studies, so I am certain you are highly skilled and capable. Even if your PhD hasn't been the best experience it has gifted you in many aspects.
It doesn't matter whether your supervisor believes in you or has given up. Regroup, finish that paper and prove her wrong. More importantly, prove to yourself that she is wrong about you.
In my case, I am choosing to believe my supervisor is finally giving me the space to build my own ideas and focus on finishing this beast. Trying to turn his apparent loss of interest into positives. My perception may change in a month or two, though...
All the best to you
Hope it gets a little better!

+1 particularly for "think less about what your supervisor thinks of you"

I was in a similar situation as you and I graduated with my PhD last year. In my situation it was me who got rid of the supervisor. Despite being a nice guy he was simply terrible at getting any work done. All the other PhD candidates had sacked him as well before me finding out about his track record.
Losing supervisors happens all the time. In my PhD two supervisors left for other jobs, one was sacked and only by sacking one did I get a much more competent PhD supervisor, who also ended up leaving but just as I was completing. I wouldn't have passed without his support. There was also one who tried to insert herself into my PhD but was told where to go when she displayed a dismissive attitude in conjunction with a lack of competence.
You should maybe reframe your situation, because it doesn't sound like you had a good supervisor in the first place.
I also had to work on my PhD for two years after funding ran out. That's the priority, find an income. I am not sure how it works where you are but you certainly wouldn't be allowed to claim unemployment benefits while doing a PhD in the UK.
Most people go through something similar simply because they let anyone supervise PhDs. One candidate who started when I did is supervising and I don't think that's a great idea based on her lack of experience. From what I have seen nothing seems to happen to bad supervisors, the one I sacked is still messing up other PhD candidates' work.
It's your PhD so take control of it, passing is more important than whether you upset a supervisor or three. The right supervisor will get you over the line, an incompetent or inexperienced one will just shove more hurdles in your way. Always ask how many completions they have as a guide to their effectiveness.
In terms of writing a paper, it shouldn't take a year. There is either a technical writing issue which can be easily addressed, or it another issue which is that you are striving for perfection which isn't possible anyway. Many academics can be obsessive in nature. It's an issue if it interferes with task completion. Finish a full draft which isn't perfect, get feedback on it and move forward.
My impression is that you may have obsessive compulsive traits which will likely be the root of you questioning your abilities and holding up your work. The fact you have been working on a paper that long makes this likely. This can easily result in distress. Addressing this may also be a priority in terms of completing your studies, and career, however with the right help that can be overcome.

In my situation it was me who got rid of the supervisor - this is to something that you can do in Germany. You may of course attempt to switch supervisors but it has to be a move where everyone is comfortable. I switched supervisors after my first year to get one who was better suited for the kind of research I was into, but they were very good and long friends so the transition was completely smooth (it was my initiative, though)

Adding to the answer provided by coffee_into_plots and WhatTheDuck: There should be an ombudsman/ombudswoman for PhD students if you are at a German university. They are there to help the students and mediate if there are issues between you and your supervisor. This might not help but its free and worth a shot.
Depending on your contract and research: If you cannot finish before your contract runs out it could be an option to finish your thesis while unemployed (receiving unemployment benefits). I absolutely hate that PhD students have to fall back on this option but I know several people who finished this way in Germany. Maybe this lets you finish without having to gain your supervisor's trust back.

first of all, do not be upset. this is very common for any PhD student.

rethink why you want a phd - do you want to be a professor? do you enjoy the academic research? how a phd would benefit your future career or life? Phd is an expensive investment and you have to convince yourself that it's worth the time and effort. I had classmates spending 8 years on his Phd. It is okay as long as you know what you want to get from this experience.

if you are determined to get a phd - calm down and make a plan. there are many ways to make progress, such as talking to your professor to get her support and advice, making a research plan, or, the worst case, working with another supervisor. Professors usually do not give up on their students if they notice their hard work.

if you have not published any articles and it is a mandatory requirement, you need work on it right away. there are many places to submit your articles - some favor theory and method and others favor applications.

stay healthy.

From what you write (and of course, I do not know the details), it sounds like you should seriously think about quitting your PhD.
Without a very strong PhD, it unlikely that you have a career in academia, and I have seen to many people moving from PostDoc position to PostDoc position and then eventually leaving academia at 35 or 40.
On the other hand, outside academia it often does not matter whether you have a PhD or not.

You have to decide, whether you still think you are going to finish your PhD successfully. This has two aspects:

Are you able to do so? I.e., knowledge, funding, health, research idea will provide some publishable results.
Do you still want to finish your PhD? Can you suffer for two more years, dedicate your time, life, thoughts at night to your PhD? Or are you okay with moving on and looking for an industry job?

Talk to your supervisor whats needed to finish and if they think you are going to achieve it. Otherwise, how could they support you with an exit strategy like writing a positive letter of recommendation, handing over your work to someone else, keeping you employed so you can finish your paper, and apply for a new job.
Aborting a PhD is always a possibility. Don't make the mistake of sunk cost fallacy. I know several people that regained happiness in their life after moving on and taking a job instead of persisting on the PhD.

My honest advice to you is yo pack and go. You have been writing a paper for 1 year and you reached your 4th year without achieving any significant milestone. Not everyone is cut for a PhD. Sorry!

I don't think this is helpful advice. Timeframes differ a lot by discipline and country so little can be inferred from the length of time that paper is being written, and your statement that they have reached this point "without achieving any significant milestone" isn't evidenced (and is uncharitable).

Four years ago…have you forgotten there was a two/three-year-long pandemic? That slowed progress for millions of people all over the world.


text:
Should I include the article I co-authored in my resume?
I studied a specific topic with my professor in the intern researcher scholarship program in college. One of my friends also was helping me. He was planning to become the professor's research assistant, and in the meantime, was helping when he had his free time. I prepared an 18-page document and conference paper. After that, we continued with the same industry, but he continued academics, and I continued on the field. Then, he started a master's degree and became a research assistant. His topic decided as the expand the current work we worked on make it more and more detailed. Last year, his paper was published, and thanks to him, he added me as co-author.
Now, one of my plans is to continue on the academic. Should I put the published articles on my resume? If it is yes, how should I put it?
Since I am continuing in the field, my experience and knowledge about academics are low in my current situation. That's why, If this question is an absurd one, I would love to know that. Thanks.

Congratulations on your publication!
And yes, absolutely, do put it in your CV! Academics typically have a subsection "publications", possibly even as a separate document. Especially if you have been around for a while, this can become quite long. However, at the beginning of your academic career, it might make sense to have it as a subsection of your "general" CV, unless wherever you submit it requests a separate list of publications.
I personally format this list in exactly the same way as a list of references in any paper, but in descending order of publication date, so the most recent one is the first one. Also, depending on your field, how many co-authors there usually are and whether the position in the list of authors is relevant, it may make sense to typeset your name in bold.

I agree and yes, put your name in bold. Your coauthor's name will come first.

Yes, publication lists can become quite long.  My father has almost 1000 scientific publications.  He just links to an online list of them.

Yes, list any publication in your field for which you are an author. Even fairly closely related fields work for this.
A CV normally has a Publications section, generally near the top.
Only if the publication is wildly out of field would I not list it. I actually have rather diverse publications (and am working on another) and won't list a few of them on my CV for anything related to math or CS.
The CV is intended to highlight your accomplishments in the field as this surely does.

Why would you not add a particular paper to a CV? Surely it's more important to show a track record rather than picking and choosing (assuming you're not an academic with 50+ publications under your belt)? Plus, even a publication completely unrelated to your chosen field demonstrates that you can go through a peer review process successfully, right?

@isolatedmatrix To give examples to exclude publications from a professional CV: Donald Knuth's 3:16 Bible Texts Illuminated. Or if you publish your hobby as cyclist, dog breeder, Lego brick builder, report to your local newspaper from comic con.

@usr1234567 I'm not sure I would consider an article in your 'local newspaper' a 'paper', or a book about religion... In case I wasn't clear, I was asking about why someone might not include an academic article in a CV, assuming it's not saturated with articles already.


text:
Will last semester grades before applying for PhD programs affect my chances?
I'm a student studying Industrial Engineering at a strong public research university in the US well-known for engineering, especially my field.  I'll be applying to PhD programs this upcoming fall but have concerns about my current semester's grades.
My performance before this semester has been solid (3.8+ GPA, Dean's list all semesters, only 3 Bs in non-major related courses) and I have been told my application is very strong (Goldwater Scholar, 1-2 publications, 7+ presentations, 2-3 years of university research, compelling extracurriculars, close relationships with recommenders who are well-known in their field).
However, this semester there is the chance I'll make a C in one of the hardest classes for my major.  I don't have any excuse for this, I simply underestimated a highly weighted midterm.  I'm trying my hardest to not have that happen, but how would it affect my chances if it did?
I'm particularly interested in how it would look when applying to a non-IE program, as I'll be applying for Stanford's Aeronautics and Astronautics PhD program - two professors have labs at the intersection of aerospace and IE that align well with my research.  Thank you for your help.

It is pretty unlikely, though not impossible that a late, lower, grade would affect anything. Most decisions are made already before final semester grades can be made available.
It also seems to be the case that some final semester chaos is expected by those interviewing and making decisions. They probably went through something like that themselves, making applications and future planning.
But it is what it is. Perhaps talk to your professor to see what you need to do to bring it up a bit.
If you apply only to Stanford then you might be disappointed. It is much better to cast a wide net for graduate study, rather than a narrow one.

Oh, I haven’t applied yet — I’ll be applying this fall.  I’ll definitely be talking with my professor to see what I can do to improve, but I appreciate the reassurance.  I will be applying to two other programs, my home lab (which has already given an unofficial return offer) and another institution with a professor I know well.  I’m not putting all my eggs in one basket!


text:
Self-plagiarism of thesis for public report
I am writing a non-academic report based on the research I did for my PhD thesis. The report is a condition of the funding that supported my research. It is non-academic and will be published publicly.
Much of the work in the thesis has also been published or is under review as journal articles or conference papers. This has been declared in the thesis in line with the guidelines of my institution. The thesis is awaiting a few final revisions so has not yet been submitted.
My questions are about reproducing the work in the report:
1) Where the public report includes results from the papers, the papers have been referenced in the normal way, and any direct quotations identified as such. Should I ALSO cite the thesis in these cases? (My initial view is that this would be unnecessary.)
2) There are sections of the report, particularly in the introduction and conclusion, that could be written by cutting and pasting paragraphs from the thesis, with some editing to maintain the flow, etc. Obviously, in an academic publication, this would be self-plagiarism, but is this an issue for a non-academic report? Would this be considered self-plagiarism? Could it be covered by a general citation ("Some of this report is reproduced from (Author, Thesis Title....)" or "Some passages have been quoted verbatim from the following source.....")? Or do I need to rewrite / paraphrase these paragraphs?
3) Neither the report nor thesis have yet been published. It is likely that the report will be published before the thesis is published, and possible that the report is published before the thesis is submitted. Would I therefore need to cite the report in the thesis, to avoid self-plagiarism in the thesis?

Are you listed as an author of the report? If not (since it does not list individual authors but only the institution, ...) I would be more careful. Someone could mistakenly(!) assume that you plagiarized that report since your authorship is not visible.

Yes I am listed as the lead author @J-Kun

Almost all questions about plagiarism come down to the question of what expectation of originality the documents carry.
In particular, a funding report doesn’t carry the same expectation of originality that either a journal paper or a thesis would.  It’s very common, and legitimate, for a funding report to consist (partly or entirely) of material re-used from other presentations of the work.  (At least, this is the norm in my experience in maths and theoretical CS; I can’t speak for all fields or all funding bodies, of course.)
So it should be absolutely fine to re-use material from the thesis or paper in the report; and I’d feel it’s fine to use a blanket attribution like “some parts of [or “much of”] this report are based on [or “taken from”] the corresponding thesis (Smith 2020) and paper (Smith and Jones 2019).”

It is likely that the report will be published before the thesis is published, and possible that the report is published before the thesis is submitted. Would I therefor need to cite the report in the thesis, to avoid self-plagiarism in the thesis?

It certainly doesn’t hurt to do this.  But it’s common, and understood, that the chronology of publication may not match the chronology of production, so there’s no need to make it sound like it detracts from the originality of the thesis.  It can be given as an aside, and phrased as e.g. “The report (Smith 2019) contains material excerpted from this thesis”, or similar.  Conversely, the report can and should still cite the thesis in this case, listing it as “(in preparation)”, “(to appear)”, or similar.

I guess that should read "almost all questions about self-plagiarism".

@Uwe I don't think that such a restriction is necessary. If you publish a paper in an academic journal then the expectation is that it is all your own work unless you specifically state otherwise; if you are chatting to someone in a bar about what you do there is no such expectation. In the first case you must carefully cite all the work of other people that you make use of; in the latter case, if you do, no-one will ever want to chat with you in that bar ever again.

1) Where the public report includes results from the papers, the papers have been referenced in the normal way, and any direct quotations identified as such. Should I ALSO cite the thesis in these cases? (My initial view is that this would be unnecessary.)

Cite both, especially when the thesis extends (as it most likely does) the paper.

2) There are sections of the report, particularly in the introduction and conclusion, that could be written by cutting and pasting paragraphs from the thesis, with some editing to maintain the flow, etc. Obviously, in an academic publication, this would be self-plagiarism, but is this an issue for a non-academic report? Would this be considered self-plagiarism? Could it be covered by a general citation ("Some of this report is reproduced from (Author, Thesis Title....)" or "Some passages have been quoted verbatim from the following source.....")? Or do I need to rewrite / paraphrase these paragraphs?

A thesis isn't considered as "published," so it can be treated similarly to a technical report or draft, hence, you can recycle material.

3) Neither the report nor thesis have yet been published. It is likely that the report will be published before the thesis is published, and possible that the report is published before the thesis is submitted. Would I therefor need to cite the report in the thesis, to avoid self-plagiarism in the thesis?

You can state in the latter document: Parts of this thesis/report previously appeared in [X] or A preliminary version of this thesis/report previously appeared in [X] or Report [X] includes a summary of these results or ...

Always cite yourself in any published work. Since the work is yours, however, you can quote extensively from the thesis, but make sure you indicate it as a quote. Paraphrasing doesn't mean you don't need to cite.
However, in a case like this, as long as no confusion could result in who did what or where the original material can be found, you can probably use a general citation. However, I'd still "quote" it as appropriate if you copy from it. Even a footnote that says that quoted material is taken from ... would probably be fine.

Thanks @buffy I just added a 3rd question - what if the report is published first? Should I reference the thesis in the report in the same way?

I don't have a good answer for that and I've been seeking one. I guess I'll just defer to user PLL for that question. Best to have the report cite the thesis, but maybe necessary the other way round.


text:
How do I reframe getting an MPhil instead of a PhD the first time round, in the context of applying for a mathematical postdoc?
The Question:

How do I reframe getting an MPhil instead of a PhD the first time round, in the context of applying for a mathematical postdoc?

Background:
I tried for a PhD in group theory at respectable university in England; however, the pandemic, a lack of funding, and the onset of schizophrenia meant I had to leave with an MPhil.  I got a paper out of it in a pretty good (Q2) journal.  The project, I feel, was taken as far as it could have been, given the state of the art: the open cases were similar to those in related endeavours.
It feels like a failure.  It took me five years full-time to get that MPhil (though around a year of that time was spent off for health issues); typically, a two year degree.  I passed my viva with minor corrections.
Currently, I am studying for a PhD, again in group theory, at a university in Scotland.  I'm in my second year.  (Since this is a UK degree, the maximum duration, as you might know, is four years.)
I still have schizophrenia.
Why ask?
I want to prepare for postdoctoral applications early.  I did my best here to put the MPhil in a good light (bar thinking of it as a failure) but it feels inadequate.
Application committees are likely to ask about the MPhil.
The most I can say at the moment is: it just wasn't the right time for me.  That's a platitude, sure, but it applies.

People evaluating your applications will be interested in what you've done and what you plan to do in the future. It seems unlikely that they will be terribly interested in having you "explain youself" or dissecting why exactly your previous attempt at a PhD did not work out if your current one goes well, since this has no bearing on whether you will be a productive postdoc or not. I am confident that the actual underlying issue here is how you can learn not think of your previous PhD as a failure, because I assure you most people will not care about the minutiae of your educational history.

Particularly the whole Covid thing made lots of plans go kaboom in many different ways. Postdoc applications will focus on your PhD work.

To clarify, this is no issue if hypothetically you apply for postdoc just after you finish your phd right?

Yes, @BCLC. I think it's okay.

I don't think you have to frame it or reframe or anything, instead focus on your accomplishments and what you'll do next in your applications for post docs. Since you haven't finished your PhD yet, that's the most important thing: finishing the PhD and securing accomplishments in research (publications, etc) while doing so.
The place the previous failed PhD may have hurt you was in getting another PhD program to take you on and believe you can finish. You've done that, so congratulations, it's in your past now. If you dwell on it rather than focusing on what you still have in front of you that's only going to hurt you


text:
Leaving tenure track position
I'm a relatively new tenure-track professor considering leaving my academic institution for another academic institution or a non-academic job in the not-too-distant future.
I have two questions:

When to Inform Colleagues: If I decide to leave, when should I tell my colleagues, both in my department and outside? I want to avoid any backlash but also give enough notice.

General Advice: Do you have any tips or suggestions on how to handle this?

Any insights or experiences would be very helpful. Thank you!

Also related: I want to leave my tenure track position before fall. I have great prospects but no new position "locked up": when should I break the news?

Welcome to Academia.SE. Your question is so vague we can't really help you -- what part of the world are you in? What type of institution? Why (generally) do you want to leave? Will you resign before or after you have another job lined up? As it is, we can't really add anything to the linked posts, so your question has been closed. However, if you want to [edit] your question to provide more details, we may find that there is a distinct question here. Good luck.


text:
What are the platforms to monitor for academic job search (Tenure Track/ Long-Term Positions) in the Sciences?
Apart from common websites, like Chronicle of Higher Education or Higher Ed Jobs, what are other platforms where academic positions are posted?
I recently missed out on some opportunities by not being on a list-serv (very niche field-specific group) and also got a few opportunities by being on another similar group's email-list. I'm curious to learn what platforms others are using to keep track of open positions.

I suspect that this is very field or even niche specific, as you have found out.

Your PhD adviser should know. It's very field dependent.

Which country are you interested in?

As some of the other comments already mentioned, many such portals are field-specific. However, I can provide some examples from the field of geoscience that may help you search for similar portals in your own discipline, should it differ.

Academic Job portals: Besides the platforms you manages, some other good allrounder portals are academicpositions.com or Times Higher Education.

International professional / academic organizations: In the geosciences, the biggest organizations are the American Geophysical Union (AGU) amd the European Geosciences Union (EGU), both of which have their own job portals (here and here).

National networks: These are a step down in scale, but can be very useful, especially if you are looking for positions in specific countries. For instance, in Germany there is academics.de, for Norway there is jobnorge.no.

Vacancy pages of universities: That sounds pretty obvious, but when I was looking for a tenure position, I tracked the vacancy pages of a number of well-known universities in my field, for instance the NTNU or TU Delft. Some of them (like ETH Zürich) also allow you to set an email alert for new job postings.

Finally, I strongly recommend to ask around your network of colleagues. Many of them may have their own list of job portals to post their own PhD vacancies, or hunt for new jobs themselves. Your colleagues may not only get you onto some of the more obscure list-servs, but if they hear of a vacancy in your field, they may let you know.
Best of luck with your job hunt!


text:
Incomplete experiments, note to reviewer?
I'm submitting to NeurIPS today and some of my experiments are not complete.
I think my paper is a fair submission even without those results, but the results I'm currently waiting on would clear up the last of my own criticism of the work.
Obviously, the reviewers should only review the work based on the results I present. But, perhaps they will be less confident in a negative review if there is scope for these results. I want to write a note to the reviewers mentioning my partial results and asking them to consider waiting for our rebuttal if they see the lack of this experiment as a weakness.
I see there are discussions on doing this for linked content and resubmissions, but is it normal to do so here (and if so where shall I put it)?
In case it helps, the full story is that I lost access to the server I was using to train these experiments, haven't been able to regain yet, and am trying to hack the code to run on very limited VRAM. But with just four hours to the deadline it doesn't look like I'll be able to fill more than one or two cells in my big table.
With NeurIPS getting over 21000 abstract submissions this year, I expect the reviewer load + competition will be sufficiently high that any scope for criticism might be exploited by reviewers to quickly dismiss my work. (Maybe it will also mean that they won't care about the absence of this experiment-- I welcome your comments).

Just submit what you have. The story is unfortunate but they receive way too many submissions for anyone to care.

@user176372 yeah, that's what I ended up doing. But I regret it. I think putting something Appendix would have been appropriate. (Or as part of a justification in checklist that we have to submit along with the paper-- I feel that might be one of the first places reviewers look).

Just imagine being a reviewer, though. You've got 20, 30, 50 or whatever of these things to sift through. One of them has a table in it that is literally incomplete. I'd personally be so harried that I'd just recommend a reject immediately without parsing the rest, assuming that the whole thing was incomplete.

Hmm, I don't mean putting an incomplete table. I mean, kinda reducing the scope of the experiment to a "preliminary" one that fits the results, within or accompanied by a note.

Also, I would hope the first round of reviewers are not expected to sift through double digits of these. At least when the # of abstract submissions was 12000 @ 3-4 reviews per paper (just 2 years prior!), they were able to find 10000 reviewers


text:
Should I make project report public before publishing journal article
I have written a report about a piece of user research that was carried out with an industry partner. The partner wants to make the report public, and I would also like it to be public as soon as possible and disseminated widely as it is of interest to the (fast moving) industry.
However, i also plan to write an academic article (which will obviously take longer to publish) based on the research, and am concerned about self-plagiarism.
Should I

Wait until after journal publication to make the report public
Make the report public and reference it in the article
Make the report public and include a reference to the article ("in preparation")

Check the rules of your intended target journal(s) about their rules for posting to a preprint server. Many journals will exempt posting to a well-established preprint server from their rules about pre-publication.
If the rules allow it, post the report to the preprint server (preferably in a form close to that expected for an academic paper, but you can always call it the "first draft"; most preprint servers allow posting of updated versions).


text:
What tools do you use to manage writing co-authored papers?
What tools do you use to manage co-authored papers? This is similar to questions active 4 years ago and 5 years ago. I assume tech has changed since then.
Co-authored projects I have been on have used Dropbox to share files or shared files through many emails. This does not seem particularly efficient.
Update: In my field, almost everyone uses MS Word.
I use Trello for solo-authored work. It has the option of inviting collaborators but I have not tried it. I am also interested in reproducible workflow and have some of my code on Github. I am exploring the Open Science framework, too, but have not used it to manage an entire co-authored project.

A shared network drive and Word's "track changes" features works very well in the majority of the cases. Not every task requires new technology to be efficient.

Wait, are we speaking about actually writing the paper, or maintaining a to-do list? Because Trello doesn't help you write the paper, from what I understand.

I and my students use Overleaf.

@FedericoPoloni I agre Trello works just like a time management system or to-do list. But I think it is possible to connect the Trello to a Github repository to track your changes.

On Stackexchange the usual way to ask for an update of an existing question is to comment on the question, and perhaps leave a bounty (the latter isn't really an option for new users, though somebody else might choose to help out).
Asking another question the same is considered a duplicate. I'm not sure I personally agree with this approach, but that's how it is at the moment.

Thanks for the explanation @Flyto. I tried to differentiate my question by noting that technology has changed in the past half decade.

The best option is Github I believe. But it pretty much depends on what do you use for writing papers? Do you use LaTeX or other typing softwares like Microsoft Word or LibreOffice which is the free and open source cousin of Microsoft Word. If you use LaTeX, which I recommend it personally and probably many other people here too, you could create a repository in Github and put your tex files as well as bibliography files and then simply you could share that repository among your collaborators. The reason why I like LaTeX instead of using Microsoft Word is that tex files by themselves are human readable files in comparison to binary .doc files. As a result, you could track and maintain your version control for your paper like a code. Otherwise it's not easy and trivial to track binary files (e.g. .doc files) by Github or other version control softwares (e.g. Data Version Control (DVC)) Also, it is possible to link that repository to OverLeaf and that makes sharing/writing much easier. But for more accurate solution in order to fulfill your needs you need to mention what is your main writing software for preparing papers.

Can someone explain why downvote?!

I didn't downvote, but to me it seems very wall-of-text-y and hard to read. I don't blame the downvoter.

Our lab uses Box, largely because our institution has purchased a license for it.
I wouldn't necessarily recommend it as an ideal solution, but one advantage is that it saves a history of past versions, so if two people make edits at the same time at least you can go and get the prior version to merge them, though it doesn't make this obvious or 'automatic' the way a git-based solution would.
You can also lock files while you are editing them, but it's not particularly obvious and it requires people to actually manually lock the files, which I find people don't usually follow through with.
Outside the lab, I mostly do collaborative efforts (that are documents rather than code) with shared Google docs.

But let's say you want to share your work with a collaborator which not necessarily affiliated with your university or institution? I don't think someone outside of your institutional network could access your Box folder. But the main advantage of Github is that you could share it with people even outside of institutional network.

Besides the accessing difficulties of outsider people, the version control that Box use for binary files is not useful for papers cause the difference between current and previous versions are not comparable generically like Github when you maintain the version control for tex files. I think the Box is a good option to share the final constructed PDF file with other people not while you are actively changing the paper, when maintaining the version control is a crucial point.

@AloneProgrammer I agree it isn't a perfect solution, but neither is git. Mostly the collaborations are internal to our institution. The question asked what tools we use, not necessarily which tools are best :) The version control with box works fine with binary files, it's really no different than Git would be for binary files: you can access an older version, like one saved by another user, and manually merge them using the merge tool in Word. I've had enough trouble convincing people to use git for code, converting everyone to LaTeX from Word is unlikely to be a success.

Well..., I agree to some extent cause people, who are not familiar with coding stuffs, have some fear that LaTeX looks like a coding software.

In my experience, the important part of writing things jointly is to give everyone the time and space to write at their own pace. This means that one of the most awkward things to do is to send around a single word document to which everyone then adds a version number. That's because this mode means that only one person can write at any given time -- independent of whether that person has the time to do that right now, or whether someone else actually just had a good idea worth putting into the document. It also inevitably leads to situations where someone edits an older version and then some poor soul has to figure out what the changes were and port them forward to the current version -- further blocking everyone else's progress.
So whatever mode you adopt, make sure you have a way to ensure that everyone can write whenever they want. MS Word documents just don't allow for that, but that's not a problem: There are many other ways you can use, and in some of these cases the final version can be converted either into MS Word, or into another format that can then be submitted to whomever needs to get the document in the end. Examples that I have used in the past are:

For things that don't require extensive formulas, just use a Google Document. Everyone can add and edit whenever they want to add and edit, including concurrently while someone else is working on another section. The final version can then be exported in MS Word, OpenOffice document, or PDF format.
If you need formulas but don't know latex, just use Overleaf.com. Again, everyone can add and edit whenever they want and concurrently if necessary. The end result can be exported as PDF.
If you know latex, you can also just work on the plain latex files and share them via github. Github has mechanisms to resolve conflicts if several people started writing at the same time, starting from the same version, but commit them at different times.

Of these options, github is probably the most awkward mechanism because your changes are not recorded immediately, but only when you upload them (possibly causing conflicts with changes others have made). The advantages are that you can work offline, and that you retain a perfect version history if you ever need to find out who wrote which line. The latter seems to rarely be a concern when writing papers, proposals, presentations. The former is a concern, but is becoming less of one as everyone tends to be online all the time these days.


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Colleagues present same data analysis for years, each time with different "framing". Ethical?
I have seen colleagues present the same data analysis multiple times over several years.
By present, I mean two things. First, present the work to other faculty and PhD students in departmental seminars and informal brown bags. Second, I mean present the research to journals by submitting it for peer review.
Each time I see the work presented, the data analysis is rather similar to the last time I saw it presented. But what the study is "about" changes significantly, sometimes using different theories and claiming to have a new research question.
What does not change is that the paper claims to test hypotheses derived from whatever theory they are using. The hypotheses keep changing, but the analysis doesn't change.
The changes to the theory and research question are explained as having the previous paper rejected at a journal and needing to change the "framing" of the paper or responding to reviewers who "didn't like" the way the analysis was presented.
Is the behavior of my colleagues ethical?

How does ethics enter in to this? Maybe it is misguided, but unethical? Maybe they are just getting a deeper understanding.

It would be helpful if you clarify what you mean by "present". If it is just presenting as-in some sort of non-archival presentation or discussion, if they are changing the framing of a study and resubmitting it after a rejection, or if they are publishing year after year the same basic work - these would all call for very different responses!

Should “ethical” be replaced by “lazy”?

No, it is not ethical.

@BrianH I updated to specify what I mean by "present"

Do they just apply the same method to a new research question or do they literally use the same data and analysis for a completely different question? I do not understand how this works in practice...

@koalo They use the same data and analysis for a completely different question. I even heard one of the senior co-authors on the paper say during a presentation, "We need to find a theory that gets us to a positive relationship between _____ and _____." He said that because that was the relationship they had in their regression analysis.

One thing stands out - you say they are "changing the framing" in response to reviewers comments etc. Does that mean that none of their previous work submitted to journals was accepted after peer-review, or do they keep re-submitting work which has significant overlap (in the analysis, as you say) which was already accepted for publication or published?

@penelope None of the previous submissions were accepted.

@birch "None of the previous submissions were accepted." really?! If they don't have any published materials how they become your colleague? I mean you didn't specify your position but it seems you are a faculty, so how?!

What venue are they “presenting” the work in, and does it carry an expectation of originality?
Publishing multiple minor variations of the same piece of work would indeed generally be considered as unethical, or at best borderline-ethical “salami-slicing”.  That’s because publishing carries an expectation of originality/novelty: you’re not supposed to publish the same work twice.  This is deeply entwined with the ways that publications are used as a metric of productivity.  However, it sounds like this isn’t what’s happening here, if your colleagues haven’t succeeded in publishing the work.
Whether presenting multiple minor variations of the work is ethical depends entirely on what venue they’re presenting in (major conferences? informal workshops? the departmental seminar?) and whether it has an expectation of originality like publications would.
This varies between fields and subfields, and between conferences within subfields.    In pure maths (at least in the subfields I’m familiar with), conference presentations have no expectation of originality.  You can present the same piece of work every year for a decade, and people won’t be very excited or impressed, but it won’t be considered as unethical.  In computer science, on the other hand (again, in the subfields I know), presentations at major conferences are like a smaller version of a journal publication, and as such, are explicitly required to be original: re-using material between them would be unethical.  But in less formal settings (e.g. local workshops), again there’s no such expectation of originality, and re-use of material (with or without variation) is fine.

I upvoted your answer, it is much more comprehensive than mine...

"That’s because publishing carries an expectation of originality/novelty: you’re not supposed to publish the same work twice."  It worked fine for George Lucas...

It is difficult to say whether it is ethical or not; it also will differ based on what the conferences say (e.g., do you have to explicitly state that the work has not been presented elsewhere?). There is also a gray area here: There is nothing wrong, for instance, with a secondary analysis of previously collected data.
But a colleague who has nothing new to tell for years, has probably a much bigger problem anyway...

I upvoted your answer, it is much more succinct than mine…

Original research may constitute research containing at least one of:

original theoretical frame
original interpretation of primary material
original primary material ("data," "text," "object of analysis")
(Source: Australian HERDC standards, if in doubt use the last year that the publications were collected)

One of the responses to the imposition of Fordist-Taylorist labour conditions in "The University" has been for scholars to reduce the scope and originality of research projects.
Whether this is ethical largely depends on your discipline's and institution's ethical and employment frame work, and the tolerance of journals for similar works. For example, permuting the literary texts while keeping the theory and analytical tools constant, will probably result in rejection in a literary journal: the scope for replication is smaller in literary studies.
Outside of ethics I would suggest that this is risky from a labour and employment stand-point; that departmental colleagues, unless rigorously cynical yet highly solidaristic, are likely to throw you under the bus; and, that higher level bosses at school, faculty, college or university level are going to strongly test your belief that tenure still exists.
On the other hand, as long as the volume of papers in preparation and received for publication meet standards, and if the deficiency in originality is made up for in other papers, seeking collegial support for a difficult to bring to publication piece of research is fine. Even if it bores at departmental research seminars. Maybe they need a new coauthor?

Can you elaborate what you mean by "rigorously cynical yet highly solidaristic"?

Rigorously cynical in the sense that they’ve analysed the effort/reward ratios in “originality” and decided on that basis to accept minimised effort thereby effectively betraying their beliefs about best serving their discipline and advancement of knowledge by serving volume over science. Highly solidaristic in the sense that they have labour or scholarly solidarity for their department colleagues instead of blocking them on the basis of lack of quality / service to knowledge. Minimal originality output strategies allows departmental competitors to attack colleagues on that “quality” basis.

In light of the recent comment by the OP, I think a lot of speculation can be removed from the answer. I fully agree with the answer by PLL regarding different possibilities which he covers.
The colleagues in question have been fighting for some time to publish a specific piece of research they've been working on. None of this seems unethical:

The work has itself never been published as a peer-reviewed publication.
Changing the manuscript in response to the reviewers comments (as OP says) to improve or adapt scope, level of detail and presentation style is in fact expected.
Updating the manuscript over time with new references, but also new findings and conclusions is expected, especially if this is an ongoing work.
Presenting the work at departmental seminars is an established way to get feedback.

In fact, I have a publication now that I started to write in the first year of my PhD, started to submit in the 2nd, and finally got accepted almost 5 years after starting it initially. It was a survey paper, so I can make limited parallels, but the level of detail, target audience, presentation style, etc. have all drastically changed several times over based on the reviewers comments as well as the target journal.
I'll just echo damian's answer: rather than being unethical, spending years to publish a result probably speaks volumes about your colleague's quality as a researcher. This should also be taken with a grain of salt however, as there might be valid reasons in persisting to publish one specific result (while continuing your other research activities): see my example above, but also MSER descriptors (Google Scholar search link to show the number of citations) got rejected from many top-tier Computer Vision conferences before being accepted and popularized, and the story of early days of deep learning as one example with a really big impact.

One reason I wonder about the ethics of such long-term paper transformations is that it seems at some point it becomes HARKing--hypothesizing after results are known. I don't see how it is ethical to keep repackaging the same empirical results as different "studies" and each time claiming the original intent of the project was to test the new hypotheses, but I know that the analysis hasn't changed for a long time.


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Applying to PhD programs whose research topics mismatch my experience
I am applying to PhD program that matches the theme of my research and industrial experience. As most of field of studies, there are several topics under the general theme and my experiences are just one of them.
If PhD application is all about the relevance between targeted research group and applicant's experience, how to stand out if I am trying to apply to research groups whose ongoing projects (or done ones) are not closely related to my experience (though they might belong to a common general theme)?
To be more specific, let's say my research experience was building a pioneering application built upon several basic tasks as building blocks. On the other hand, the funded projects and main topics of the targeted research groups are focused on improving the basic tasks (efficacy, for example).

It can be an advantage. Many people are aware of the value of interdisciplinary research. Your different background knowledge can bring new views into their field. That is a good card to play.

Also: when you're applying for a job, you need to have a closer match than when you're applying as a student.  To be accepted as a student, you need to show your potential.  To be accepted as an employee, you generally need to show you can hit the ground running and be productive pretty soon after starting.

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