text:
How to deal with toxic postdoc and have independent projects?
It has been three months since I joined as a postdoc. This is my first post doc position. I work along with another postdoc to set up pipelines for lab projects. This postdoc that I working along has more years of experience as postdoc but he is also new to the project that I am currently employed. Initially, he helped to get familiarized with administrative formalities like setting up an account to run things in the cluster etc. In the first few months, I started running each step in the pipeline and checking each step. As time passed, he became impatient and he discussed with PI and gave the data to another bioinformatician to set up the pipeline. The pipeline has been set up in different workflow system and it would take weeks for us to understand how the pipeline works.
I started working independently on the pipeline as I like to understand the errors in each of the steps before I proceed to the next step in the pipeline. Now, I am close to setting up the pipeline. But, this postdoc feels that I am wasting my time and insists that I follow blindly the pipeline set up by another bioinformatician. It seems difficult for me to work with this postdoc as we follow different methods to finish our work.Sometimes, I have to explain why we see the errors and it takes a whole lot of my time. He also tries to get information from me about the pipeline and does not share any information about the project. I am sidelined and made unaware of the things happening in other projects.
To avoid conflicts with this postdoc, I have started maintaining a digital lab book, in which I update my work. So, time doesn't gets wasted in explaining about the pipeline. I am also going to present the pipeline that I have been working in our lab meeting (to the lab PI and all the members in the lab). I am also going to suggest that scripts that we work in the lab will be made available in GitHub. So, with inputs from the lab presentation, we have one pipeline to follow for our projects.
I am planning to get an appointment with lab PI and tell him that I am interested in independently working on projects. How do I also tell the PI that I have problem working with this postdoc?. Sometimes, my whole day gets wasted dealing with this postdoc. He thinks that I should discuss  every step with him. But, I am ignored and not copied in some of the mails. Can someone advice on how to deal with this kind of situation
I didn't use the word 'toxic' just like that, it is because I am being ridiculed for doing my work. For example, when I send query mails to some of the forums which work on the workflow, he would comment it as stupid and unnecessary. He feels that I should check every step with him, before I start running it. If I have to more specific, I would say this as patronizing behavior.
Thanks

Sounds like differences of opinions. Why ‘toxic’?

Your lab PI has a vested interest in making sure his lab runs smoothly so that he can do high quality research. That involves ensuring good research takes place, administrivia is addressed (e.g., supplies, bills, approvals, etc), recruiting, and—among other things—addressing personnel issues. As you can probably guess, the last item is probably not the PIs favorite thing to deal with, but it's definitely on the list.
To that extent, if you have an issue, feel free to bring it up. That said, make sure you really clarify exactly what the issue is. Reading your description above I have no idea what the actual issue is (you don't like him? he doesn't like you? one or both of you is doing bad work? trust issues?) or how to deal with it. If you have a complaint, make sure its meaningful, make sure you can state it concisely, and bring at least one recommendation on how the PI can help fix it.

I'm bit concerned with people just slapping a "toxic" label on this kind of behavior and calling it a day. What if it was a PI? "How to deal with a toxic PI not letting me do things my way"? Convincing others there's value in what you do is a big task, don't just take it for granted and communicate.
And yes, do bring it to PI, outline what you are doing and why. Your coworker postdoc does not see how what you are doing will help the project move forward and it is perfectly normal. They are not being particularly constructive with that, granted, choosing to sidetrack you instead of trying to coordinate efforts but I'd argue that burden is on you (and PI).
My point is, there are generations upon generations of scientists who grew up meeting and fighting active resistance to new and shiny techniques from their peers. I'm sorry you feel that way, but it is the bulk of your work as a scientist to clearly show the advantages of new approaches. Sure, getting really good new ideas is hard, but if you somehow thought scientists are supposed to be super progressive and immediately adopt new and better ways of doing something that everyone else outside of academia does already - sorry to disappoint. It is very often not the case, and I'd surely object to it being called "toxic". With how thin resources are, some things considered great in industry like CI/CD commonly don't work at all in academia.


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What to do if own theory gets not accepted by community?
Inspired by a recent question regarding Crackpot research paper, I was asking myself, what to do, if you have a new theory or approach but it is not accepted in the community? You are not allowed to speak on conferences, your papers are rejected, and your voice is not heard in your scientific community.
What can you do? What have others done?

What do you do? Accept it and move on. It's possible to be wrong. Science is no merry-go-round where everyone takes turns being right .

In a crack-nut shell: A theory is not accepted because you convince colleagues that it is right, but because you have closed all holes through which colleagues are able to show it is wrong.

@CaptainEmacs: Or, to phrase it differently: My theory is not accepted because I cannot convince colleagues, but because all holes are closed through which I could convince colleagues to show it is worth discussing it. (actually, I don't have a theory, but for the sake of the argument)

@usr1234567 Not sure I understand.

@CaptainEmacs: You phrase as an active process (you have closed all holes), while my sentence is passive (all holes are closed) as the editors / reviewers / community does not allows the "crackpot" to have the discussion in the first place. And I have to admit, that might be a point of view.

@usr1234567 Before one can try to talk to anybody, one first needs to learn the language they speak. If you barge into a party, do not expect to be welcome, even if you are the most dazzling party lion. First, find a way to fit in. So, it goes without saying that one needs to walk the walk and talk the talk. It is very rare that people can get accepted swiftly into a community. I have contributed publications outside of my main line of expertise, but made a point of understanding precisely how the community I published in is speaking. Most crackpots don't even bother trying.

One more thing. Does their work address an actual problem? What I found with crackpottish ideas is that people espousing these ideas claim to solve a problem with handwavy statements which do not prove anything that is not already known, which do not make any new predictions and which are just repackaging old knowledge into new terms without adding new quality; this is in the very best cases - in the worse cases, these theories simply do not say anything concrete but can be fit ("nostradamicized") to match any data one likes.

@CaptainEmacs. My question should be general. The actual instance of the problem is tricky: a guy wrote a PhD in physics with a professor in physics department and they know the language and how the game is played. Beside their ignored idea they are able to publish, get grant money and so on. I am not in the field, he just told me that it happend to him 20 years ago.

@usr1234567 Sorry, but it is really not general. Too much depends on the concrete case and situation. A fellow student thought he found a (short) proof to the 4-colour theorem. His prof looked at the proof and couldn't find a mistake, until they realized that a "theorem" the prof gave in the lecture and which this proof relied on was actually wrong the way presented. This was an honest mistake, but everybody played the fairest game possible. Nobody thought the student was a crackpot. Your friend may have had a good result suppressed, a useless or nasty supervisor or simply...

... completely overestimated their expertise. There is no general answer for this. All of these happen. A PhD means that they have the basic education to be a researcher, it does not say much about their ability to judge their own work well. Not saying that it's bad. They also may have been in a particularly cutthroat community? In which case, moving to a nicer community in a neighbouring field may be a solution. Or you have one really good insight or solid work followed up in their remaining life by crackpotism. Such - quite well-known - cases exist.

@CaptainEmacs "His prof looked at the proof and couldn't find a mistake, until they realized that a "theorem" the prof gave in the lecture and which this proof relied on was actually wrong the way presented." I'm no mathematician, but that might still be publishable? You'd just be taking the untrue theorem as an axiom, so might just wind up inventing an entirely new field of mathematics (e.g. Euclidean vs non-Euclidean geometry).

@nick012000 No, it was based on a wrong theorem. You would have to isolate which axiom implies that particular wrong theorem result; and it's unlikely one of the usual suspects (i.e. axiom of choice) could be isolated (I haven't seen the proof, but I'd be very surprised if that'd be the case). It was just a wrong theorem, nothing interesting and from a wrong theorem you cannot prove anything, or rather, everything.

It is usually not the theory or the approach that is criticised, but the lack of evidence or scientific rigor.
If your theory or approach does not get accepted by the community, you should provide more evidence to convince them. If the proof becomes so good that the theory is no longer controversial, it will be accepted. This is how science works.
The stories you may hear about brilliant scientists not being believed are a typical case of survivor bias. Most crackpot theories are made by crackpots.

I upvoted, but it is not entirely true that "If [...] the theory is no longer controversial, it will be accepted." As Planck said: "A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it" - I do not think this is always the case, but there is a good amount of truth in this. However, remember: Being a genius may mean that people do not recognize your theory. But having your theory rejected does not imply that you are a genius.

Let me suggest a somewhat broader point of view. We are mostly thinking about "the scientific method" and "the scientific process" in terms of observations, proofs, theories and so on. However, as it is clear from other discussions here, there is a great amount of "soft-skillish" element involved, as with any activity that concerns communication.
As such, "a paper" is a way to communicate / spread our ideas, and if some theory of ours doesn't take roots, it means that we aren't very efficient communicators. Thus, even if a theory is eventually published in a respected journal, still a bumpy publication road may indicate that our way of transmitting ideas isn't particularly appealing.
Therefore, there is certain psychology involved, too. For the sake of the argument, suppose the theory I am pushing forward is sound. Even in this case, people are wary of "grand theories", where they first have to accept certain premises, and then see what kind of great building is being constructed in front of them.
I'd say that a more pragmatic approach would be to attack specific individual problems and show that you can solve them. Yes, it might be based on a certain (unknown or unaccepted) theory, but why bringing it in right away? Here is a problem, here is my solution, answer obtained, knowledge increased, everyone happy. After several success stories of this kind one might try to unify them all under a certain common umbrella of a "proposal" or "presumption" and let it to take root.
In other words, we should remember that we write for the reader. Why readers should care about our theories or take time to ponder whether they are sound or not? Readers seek something for themselves, and the best way to push our agenda is to show how it aligns with possible goals of our readers, and give the readers tools for their tasks in bite-size chunks, if possible, without overwhelming them with grand structures.

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Good way to present long questionnaires in methods?
I'm writing a paper (my first one) in a standard article form. I must use A4 pages and a single text column.
In Methods and Materials, I must present a 23-Likert item long questionnaire that was used in the research. The problem is, I can't find a way to fit all 23 items in a concise table or image, it always ends up as a behemoth that takes up 2 pages and doesn't really fit in.
Is there a better, concise way to present said questionnaire?

Did you already present this questionnaire to the audience (that will be answering it) in some other form?

@AntonMenshov Yes, I already have the distribution data plotted in a horizontal bar chart.

No, I mean, how did you present this questionnaire while you were collecting data?

@AntonMenshov It was done through Google Forms.

Why should the entire questionnaire be reproduced at all? Just describe it in an abstract manner. What is it about, what scales do you use, how is it administered, how did you work around error/bias, what's your response rate, these kinds of things...

@henning That could be a good option, since I'm going to present each item in the result charts anyway... But doesn't this make the methods a bit vague? Is it fine to prompt the reader to view the questionnaire items in the results section?

Does 'padronized' mean 'standard' here? Can you add supplemental material to the paper?

@Eduardo Cola have a look at how published research papers (journal articles) describe their survey methods. If the survey has more than three items, nobody describes the individual items in any detail. Instead, the full survey is sometimes available as an online appendix, if at all.

@Anyon sounds like a Portuguese malapropism of standardized.

In any case, if this is an assignment for a class, it's best to ask your instructor what the expectations are.

@Anyon Yes, sorry, will edit.

@Anyon I can't add supplemental material to this particular paper, that's why I was looking for ways to better present the methods.

@henning I will probably overall skip it, since the items are presented in the results anyway. Thanks for the input.

Twenty-three items isn't that long

As I mentioned in the comments, 23 items isn't that many, unless the items are very long.
Here is how Hurley et al. (2006) introduces the 35-item Broad Autism Phenotype Questionnaire (it continues onto the next page):

As you can see, it is typeset smaller in a sort of table. I am not sure why they repeated the scale 1 2 3 4 5 6 on each row, as it is identical for each item.  Since you are limited to one text column, put 12 items on the left and 11 on the right.
At the bottom of the table, the asterisks are explained:

***Casual interaction with acquaintances, rather than special
relationships such as with close friends and family members

The questionnaire must be published in order for the results to be credible. The table is a good example. I have used an Appendix.

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Thinking about leaving academia for good. I am feeling guilty and disappointed in myself. Any thoughts/advice?
I have a PhD in mechanical engineering and am currently a postdoc. I have been fairly productive in my research, published fair amount of papers during my 5 years PhD and 1.5 years of Postdoc experience. I feel confident that I can keep publishing quite more in the coming years too.
But the truth is, I don't feel the point of any of this. I don't feel that even if I get an academic job, I can survive the constant pressure of securing grants, doing exciting but not groundbreaking research, feeling disappointment when submitting to medium impact journals, being overshadowed by successful colleagues.
When it comes to industry research, the positions in my field are hard to come by. I am an immigrant in the US and most of the positions require permanent residency or citizenship. I have been facing constant rejection for the past year. Also, I feel that my motivation to do fast paced research has reduced significantly since I graduated my PhD in 2020.
I have been considering non-academic jobs like data science (bit unrealistic) or software developer (more realistic, after taking a boot-camp or something similar). However, these will not make use of my PhD background and field of study.
Alternatively, I am thinking of going into scientific editing and communication with hopes of transitioning into a business development role. This will somewhat keep me connected to science and my field but away from the bench.
However, one thing that stops me from making a decision is the feeling of guilt and failure to achieve what I had planned when I started my grad school journey. I wanted to be a scientist, innovate, satiate my curiosity,  helm a lab and be someone that plays an important part in the society.
Now, I don't know how to move past my feelings. Any advice?

Please don't write answers in the comments. This question asks for advice; therefore, any advice should go in the answer box, not the comment box, as discussed here. A few clarifications have already been edited into the post.

There is concept in the business world known as "sunk cost".  The idea is to avoid the reasoning of "since we have already invested so much into this failing project, we should keep pursuing it."  Instead, it is best to view the next decision as independent (i.e., we have $100 to invest, should I put it into a failing project or put it into something new?).  Romantic relationships often extend too long for this reason.
In this case, I think you need to ignore the "sunk cost".  Instead, take some time to think about what it is you really want to be doing.  It's very possible your feelings are related to mental health (pandemic, burnout, poor sleep/diet, etc.) and actually have nothing to do with being a "failure".  You may find you'd prefer to run an ice cream shop.  If so, I'd start position yourself to run an ice cream shop.  Instead, you may realize that mountains are climbed one step at a time, and you may go easier on yourself that you aren't a "top performer" (yet).
My last tip would be to keep a daily journal for the next 40 days.  At the end of the day, write three things that brought you 'consolation' (i.e., joy, happiness, etc.) and three things that brought you 'desolation' (i.e., sadness, anger) from your day.  You'll likely notice a pattern which could help you make a move.
Good luck.

I'm not in the exact same situation as OP but your tip is resonating with me and I think I'll give it a try. Thank you.

you last tip is very good .. I'll try this. thank you

I wish more people who want to open ice-cream shops would.

But the truth is, I don't feel the point of any of this. I don't feel
that even if I get an academic job, I can survive the constant
pressure of securing grants, doing exciting but not groundbreaking
research, feeling disappointment when submitting to medium impact
journals, being overshadowed by successful colleagues.

To be honest, you will have similar pressures outside academia, so general dissatisfaction with things like this is not a great reason to leave academia if you are doing well.
I have 9 years of experience in my field and still haven't been able to obtain a "senior" position, while I see people with a couple of years of experience earning twice as much as I do. It's soul-destroying!

When it comes to industry research, the positions in my field are hard
to come by. I am an immigrant in the US and most of the positions
require permanent residency or citizenship. I have been facing
constant rejection for the past year. Also, I feel that my motivation
to do fast paced research has reduced significantly since I graduated
my PhD in 2020.

Outside academia, you will also face constant rejection. For one reason or another, most companies will not want to employ you. But some will still string you along for a long sequence of interviews. Many will ghost you (this is a much worse problem than in academia.)

I have been considering non-academic jobs like data science (bit
unrealistic) or software developer (more realistic, after taking a
boot-camp or something similar). However, these will not make use of
my PhD background and field of study.

That is true, but such jobs will make use of the fact that you have learned how to learn things, which is an incredibly valuable skill! Many people in many fields are not very good at this.

Alternatively, I am thinking of going into scientific editing and
communication with hopes of transitioning into a business development
role. This will somewhat keep me connected to science and my field but
away from the bench.

I did have a friend who went this route after his PhD in mathematics, but he gave it up after a while. I have the impression that it's much less realistic than the other suggestions you make above. So I wouldn't put all the eggs in this basket.
If you are interested in scientific communication, I suggest you begin by starting a blog and see how long you can keep it up.

However, one thing that stops me from making a decision is the feeling
of guilt and failure to achieve what I had planned when I started my
grad school journey. I wanted to be a scientist, innovate, satiate my
curiosity, helm a lab and be someone that plays an important part in
the society.

Well, this is the sunk cost thing, indeed. I also spent my entire life trying to be an academic, and I still feel guilty about giving it up, 10 years later.

Now, I don't know how to move past my feelings. Any advice?

It sounds like you are doing well in your academic career, so congratulations! I would do a bit of research, speak to any contacts you have in industry (particularly former academics) and try to learn about what their work is like. Take some programming courses if necessary, so you don't feel like you would be starting from zero.
Find out about routes which people took out of academia. Don't be afraid to ask people about their experiences. Most will be happy to help you.
Don't be discouraged by the constant job rejections. It's tough at the moment, and just as bad in industry as academia.
Don't throw money at a therapist unless you really think it will help. Americans think therapy is the answer to everything. I recommend talking to your friends first.
I know people who left academia after a postdoc or two. I also know people who did research on industry, learned some useful things for their Plan B, but ended up staying in academia. Both routes are viable.

I'm gonna disagree a little with your first sentence. I think "not seeing the point" is an excellent reason to leave academia. Yes, in industry you might also be asked to do stuff that doesn't feel particularly fulfilling, but at least they pay you well for it. If you stay in academia, you better do it because you either really like the job or feel it's highly necessary.

I agree partly with @xLeitix, but I do think the point Flounderer made is is worth making, even if maybe it should be amended to add the indicated nuance. It is absolutely valid that if OP thinks that by going to industry they will completely avoid the problem, they're suffering from greener-grass-syndrom and will be dissappointed. After all, the Dilbert cartoon didn't come out of nowhere...

Don't throw money at a therapist unless you really think it will help. Americans think therapy is the answer to everything. I recommend talking to your friends first. Huh. As an American, I wish that more of my colleagues/friends/family would consider therapy. Where in the U.S. are you? Certainly talk to your friends, but if the issue is depression, anxiety, ADHD, etc, a therapist will be the quickest path to diagnosis and appropriate support.

I also wanted to be a scientist, and did a PhD in chemistry. I didn't get any postdocs, and was made redundant from my job in industry after a few years. It was a difficult time, filled with a lot of rejection.
I decided to retrain in informatics, and now I'm a business analyst working on a large data management project in a research organisation. My previous experience is useful to me every day, I'm sometimes surprised how much it helps. I find the work much more interesting than what I was doing with chemistry, and I think my potential to help society is greater now.
Only you can decide if you're happy with your current direction and staying where you are, but I can tell you from my experience that changing to something that interests you more is not throwing away what you have done, and it is not failing. According to the book "Range: Why Generalists Triumph in a Specialized World" by David Epstein, it might not even set you back at all.
Whatever you decide, I hope you enjoy the results.

There are "rockstar" or "olympic" professions, where the reward for being among the best in the world is large, and the reward for being not among the best is really bad.  These professions are a trap.
This doesn't mean there aren't clever mice who get the food from the trap and don't get trapped.  But most of the mice who try to eat from a mouse trap don't get the reward they are expecting.
The most visible members of the profession by far are the "rockstars", those who defeated the trap.  So when you look into working towards that profession, you end up aiming for the "rockstars" as the goal.
However, until you put a huge amount of effort into getting better at the profession, you cannot know if you actually are (or will be) a rockstar or not.  You don't, and cannot, have the information required to know if you are going to be a rockstar; for every rockstar, there are 10,000s or more people who are convinced they have a chance.  Determining if you are someone who has a real reason to know they will be a rockstar, or someone who falsely believes they have this reason, is not something you can test without a lot of effort.
Now, you can look at what your past peers in a similar situation discovered after putting in that effort.  These peers are people with similar qualifications and similar confidence that they can become rockstars in the profession given their place along the path to stardom.
As an example, suppose you qualify for "Americas Got Talent", and your goal is to be a pop superstar.  You can count how many people have qualified for that show in the past, and how many of them became pop superstars, and use that as a decent prediction of your chances of doing it.  Probability isn't destiny; but this provides a realistic, tested model of your chances.
So when aiming to join a for a profession, what you need to look at

The median member of the profession's status, rewards, etc., and

The winnowing rate from people starting at your point to being a member of the profession.

For academia, you are someone who has "won" each stage of what could be a path towards becoming a professor multiple times.  You probably won at elementary, high school, college, graduate school "winnowing" stages, doing exceptionally well compared to your peers.  But the same is true of almost all of your peers, people getting a PhD.  In that class, you aren't special; it is best to assume you are typical as a starting point.
You have now gotten to yet another winnowing stage; where some small fraction of people with PhDs get a tenure track position; and only a small fraction of tenure track positions result in becoming a "rockstar" professor.  If the odds of that is lower than 1000:1, knowing nothing about you other than you have a PhD, that even if you continue to work towards becoming a "rockstar" professor that you'll almost certainly not become one.
If your goal is to become a "rockstar" professor, you almost certainly won't.  Do you want to become a median professor with tenure?  Reaching that point is going to be challenging, but it is at least a plausible outcome.  Now, what is a median professor?  It is a professor at a small, liberal arts college, nowhere near a major city, spending most of their time teaching introductory classes to disinterested students.  Plus some time for research, a living wage, and some upper level classes with enthusiastic (but not exceptional) students; professors often are educated at some of the best universities in the country, but only a very small number teach there.
For your alternatives you should also look at both the winnowing rates and the median result of passing each winnowing stage.
The rewards here could be financial, social status, or whatever.
If you would be satisfied with the median results of a plausible path (with, say, at least a 5% chance of success), that path is something you should consider.  You should still look at fallback plans (what happens in the other 95% of the time), but aiming for that 5% is an achievable goal.
If the chance of success is under 5%, broaden the "success" criteria until it breaks a 5% threshold, then look at the median rewards in that 5% success zone.  If that doesn't count as "winning" to you, find another path, or find a way to up your chances above 5% (but don't fool yourself!)
This means you shouldn't get a PhD unless the process of getting a PhD (getting years to do some research while being paid to feed yourself) is enough.  You shouldn't train for the Olympics unless living the life of an athlete is reward enough.  And you shouldn't go on to do an academic career after your PhD unless being a professor at a mediocre school doing median amounts of research in a small under funded lab is enough.
Becoming a rockstar, even after insane amounts of talent, sweat and tears, is winning the lottery.  Almost nobody at a stage when they aren't a rockstar knows if they'll get there, because for everyone who is convinced they can do it, 100 are falsely convinced, and those that believe it is beyond them are going to be only marginally less likely to succeed.

Why was this downvoted? I don't entirely agree but it does redirect the aims of the OP.

You should be proud of yourself for identifying that a career path won't make you happy before sinking more valuable resources into it.
Best of luck finding a path that makes you happy.

Frankly, this paragraph in your question gave me pause:

I don't feel that [...] I can survive the constant
pressure of securing grants, doing exciting but not groundbreaking
research, feeling disappointment when submitting to medium impact
journals, being overshadowed by successful colleagues.

I think your situation is one where you would profit from a mindset change/improvement. If you were not in academia right now, but in an average IT company, your statement could be worded like this:

I don't feel that [...] I can survive the constant
pressure of procuring new customer projects, creating exciting but not groundbreaking
software, feeling disappointment when finishing medium impact software, being overshadowed by successful colleagues.

If you were in a purely teaching role:

I don't feel that [...] I can survive the constant
pressure of getting assigned to my favourite courses, teaching exciting but not groundbreaking
topics, feeling disappointment when working with medium students, being overshadowed by successful colleagues.

I hope you see where I'm going. These are just the average, regular, completely normal day-to-day workings of how academia, businesses, schools etc. work. The productive parts of your life are not always grand heroic events...
I would really encourage you to sit back a good amount of time and think about your motivations. Nothing would be worse than throwing away all you have worked on, starting over, and then ending up in the exact same spot (or, likely, worse!) not too far in the future.

I wanted to be a scientist, innovate, satiate my curiosity, helm a lab
and be someone that plays an important part in the society.

You have many, many years  - decades - in front of you. Nothing but yourself keeps you from taking it a step at a time. Changing careers now will place you in the freshman steps again and solve none of your problems right out of the gate.
Your personal network needs time to develop. This would maybe be one thing your could really shift your focus on - start collecting business cards. Learn to know more researchers, but also more companies in your field. Look for industry-sponsored projects (I know, you find this not one of the greatest elements of your work) and actually do (or at least manage) those projects.
Find areas with your customers where there is actual chance to improve things that interest you. Eventually you may be a spider in a net of relationships to the industry, to students, and co-scientists and make everything work smoothly towards an overarching goal, really improving the world (or at the least the lives of some stratum of people...).
Even if what you are doing only positively impacts the people directly around you, as a prof you might have the chance to influence hundreds or thousands of people in a positive way. That is much more than most other people can claim.

"feeling disappointment when submitting to medium impact journals, being overshadowed [...] "
Now, I don't know how to move past my feelings. Any advice?
You can stop being delusional, you can realize that you are not in the top 0.00001% of the academia that will win a Nobel prize by living in a cave in a remote region of Africa. You may be not even in the top 0.001% that will win a Nobel prize. May be you will not even in the top 0.1% that will get a professorhip in a decent university. Yes, there are people more lucky than you, better at science than you, better at publishing than you.
But then, who cares? you are you, they are they.
Enjoy your life, consider that we are human beings and not machines, we can be productive for a limited amount of time in our life (both in terms of years and hours per week) and do the best you can with this limited amount. You will have whatever impact on society and on science that you can have, no more.
Good luck!

Although academia has its problems, it's a bit of a hyperbole to state only 0.1% get a professorship at a decent university, unless your definition of decent is overly restrictive.

The OP is not being delusional at all in his message, why do you tell him to stop being delusional?

@gerrit You are right. However, only 3% of PhDs become professors. Considering the universities dimensions here noted https://en.wikipedia.org/wiki/List_of_largest_universities_and_university_networks_by_enrollment I have a bad feeling...

@SpiderRico how would you define someone that dreamed of being a scientist but is worried by the securing grants pressure and being worried by not able of delivering groundbreaking research? Research is 99% failure! All this while putting him/herself in comparison with colleagues that are overshadowing him/her: either they are luckier than him/her, so he/she should be angry, if anything, or they are objectively better than OP, so OP should not have a bad feeling about that and should take it with serenity (plus, I would be curious to see a definition of "being better").

Big life transitions are a really good time to meet with a therapist to talk it through.  Even if that's not something you want or need to do long term, a month or two of sessions right now could really make a difference in terms of sorting your feelings out about leaving academia now rather than letting it linger.  If you're having strong feelings of guilt that's a good sign that there's something you need to talk through to feel better about your decisions.

Go to industry and find out, that there are cool jobs, too. Even outside of corporate research. Being a project manager, team lead, or recognized expert can be very satisfying. And it might be more healthy compared to academia (depends on job, company, and you).
Looking back, my PhD time was one of the most pleasant times of my life: I was young, did cool research, had a great group, worked for a well-respected supervisor, got a title, met smart people, traveled to conferences, presented my work in talks.
But for me it could not last forever, thus I had to make a move. Now I don't have to think about funding, I have a permanent contract, still doing cool stuff (but completely different), I took over a lot more responsibility, and never wanted to go back.
Your mileage might vary, but I hope to give you some perspective.

Think twice, rest a little and think again.
Whatever decision you make is the right one.
Both paths have positive and negative sides. So there is no right answer, no one who can make this decision other than you, no one who can know the future. And whatever decision you make is the right one. (I know it seems to contradict itself but it doesn't really do it). It is important that you are serene about this, because you have to live with it.
Research is a drug, and once it gets under your skin, once you are addicted to it, it will be difficult to be without it. But the path you are on now, that you described so well, also gives you reasons to change: the stability of work, besides a right, is a necessary basis for peacefully building your life outside (outside the world of work). And for a balanced life you cannot have only one aspect active, because in the long-term you have to be able to expect periods in which problems arise on some aspect. Having more active sectors guarantees you that somewhere something will go better than somewhere else.
On the other hand, a job that you really like doesn't weigh in your life. Never underestimate it.
Continue publishing. I would like to lead you to reflect on this aspect as well: you state you can continue publishing by doing another job.
True for the first time, more and more difficult later, because you will not easily be able to keep your knowledge updated up to the level necessary to be able to publish where you aim, and you will find less and less time to devote to this. By making a career (or wanting to make it) your energies and more importantly your time will be focused on something else. Not to mention marriage, children, parents (including in-laws) as they age, home...
Secondary job. However, you could also decide to continue the current job and try to do as a "second job" the research on the topic you would have liked to do. Try for 4-6 months to read, digest and work on what is needed for it, and then you could have the first outcomes to evaluate.
Alternatively, you could try to walk the path you mentioned _scientific publishing and communication _ (or whatever) as a second job and see how it goes.
Final words of warning. If your soul is bounded to research  and you need to sell it for a job, do it for money!

Okay, I am leaving academia too. This is the nature of academia in the way you have described. My point is go into data science and opportunities will come and you’ll be more appreciated into the industry.
If you can go in healthcare data science, I assure you won’t be disappointed. I was wise enough to stop my PhD in the third year, started a Msc in Data Science and landed with a job in healthcare industry, in an academic sector. However, after 3 years and a half, I have been offered a job in a corporation well established and will definitely go for it.


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Different field of interest in my undergraduate projects and higher studies
I am currently a 3rd year undergraduate student in Mechanical Engineering. I have done projects on different topics. I have done a project on the performance evaluation of jet engines with different outlet shapes, making a pick-and-place robot, and some work on the application of microfluidics (the fabrication part) and also fluid structure interaction . The first and third of these have resulted in publications. I am currently working on adaptive and moving meshes and am very interested in learning more about turbulence and related topics. I have been reading about the topics, and I want to do my masters degree and PhD in this field, but I don't have any publications on this part. Will my previous work experience in microfluidics, bot making, fluid structure interaction etc. be a negative if I apply to a particular lab doing work in turbulence, turbomachinery, aerodynamics, etc.?

What country do you plan to study in?

@Buffy Mostly probably in UK or Germany

Getting into a graduate school is a multi-factor process.

Class marks are important.
Recommendations from profs are important.
Extra-curricular activities are important.
Various activities that would be labeled "leadership" are important.

You already have what appear to be quite applicable extra-curriculars. Leadership is about doing things that contribute some way to campus culture. Your projects also count in that direction.
The subjects you mention are going to be heavily maths oriented. 3-D calculus, matrix algebra, and computational methods of solving equations, just to name three, but there are more. You should swat those topics if you are not already proficient.
Your previous experience is probably not going to hurt you, especially since you got results that were sufficiently interesting to publish. Indeed, having publications is "gravy" in the sense that most undergrads don't manage to publish anything. Most profs will look at that and be pleased even if it is in another subject area.
If you can find time to do some classes in your areas of interest that will help also.
Hopefully the profs you worked with will remember you and be happy to give you a LOR.
Also, many governments (and most grad schools) have scholarships, and usually you have to apply to them to be considered. So scope out the schools you are interested in and find those scholarships. If you get one of those it is a HUGE push to getting accepted. If you bring your own funding, even part of it, most grad schools will be eager to have you join.


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Can I take questions from an academic textbook and publish them on my "question bank" website?
I have many books and worksheets for JEE (Joint Entrance Examination) in India. I want to make a website that will serve as a question bank for students. I want to take questions from these books and worksheets to use on my website.
Can I use them as such? Is paraphrasing also illegal?

The material in all those books and worksheets you're referring to is almost certainly copyrighted.  Publishing it on your website would be copyright infringement. If you'd like to use that material, you'll need permission which you're unlikely to get.  You might try offering to pay a fee for a license, but even then, I suspect the answer will be no.  People write and publish books because they'd like sell books, not license the questions at the end of each chapter.
If you'd like to create a question bank of material for which you clearly have the necessary rights, the most straight-forward way to do this would be to write your own questions.  I would avoid paraphrasing others' questions but you could certainly think of them as examples of the topics you should try to cover in your own questions.

Note that for some books, the set of exercises is actually the most valuable part. Since they guide what the student actually does, they guide learning, perhaps more than the text itself.

Also note that the ideas in a copyrighted text aren't copyrighted, only the expression. So, you can use the concept behind an exercise to write your own. But paraphrasing and obfuscating minor changes isn't enough. Think deeper as you want the students to do.

So much for chegg's business model


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Should I withdraw my paper because review is taking too long?
I submitted an article to a prestigious journal JCR Q1 about 20 months ago. It took more than 6 months for them to send the article for review. But it was worth it. The reviewers did a good job and decided "major revisions". The EiC was very kind to me and made suggestions for improvement.
However, it has now been 11 months since I submitted the revisions, and I still have not received a decision (the status remains at "with editor"). I have contacted the EiC twice and asked for an update. The first time (6 months after resubmission) she told me that Covid had delayed the process. The second time (10 months after resubmission) she told me that she was still reviewing the revisions and was happy with everything at the moment, that she thought the article was good, but required a few more weeks. She told me he didn't think any further rounds of revisions were needed. But I still haven't heard back.
I also have 2 submitted articles in that same journal that have not been sent for peer review yet (8 months since submission).
I do not come from a field where such delays are common, although the turnaround time for this journal is particularly high (the other published articles had an average turnaround time of a year before covid).
Considering that (1) this is one of the few journals specific to my (sub, sub)field, and (2) the editor seems favorably disposed toward the revised article, is it worth waiting, or should I withdraw my article(s)?
Update (15th, December 2021)
The Editor in Chief, although later than she predicted, finally informed me of her decision: The article submitted some time ago has been accepted and the other two most recent articles have been sent for peer rreview. It was worthy to wait.

Do you have a need for quick action? Or just worried about the delay?

@Buffy I am applying to postdocs, but I am specially worried about the delay

If applying for postdocs: unless there is a strong requirement about "number of published paper", it is almost the same to have a paper from 2020 published or under review. It will not be a deciding factor.
You mention you have 2 other paper under review: maybe those are worthwhile to taken back and submitted to a different journal.

@EarlGrey Thank you for your comment. So, are you suggesting that I include the "under review" articles in my CV? I was planning not to include them, just in case the information about authorship leaks out (e.g. postdoc evaluators act as reviewers of my articles).

Just to make sure I got the timeline right, was it roughly a month ago that the editor told you they needed "a few more weeks"?

@TooTea Yes, it was around 4 weeks ago (4 weeks and 5 days).

@Naorp97 Blind review is a "best effort" sort of thing, and shouldn't constrain you outside the review process. If you feel that your paper's chances would likely be harmed if your identity as author was revealed then that's a different sort of thing, but otherwise don't bend over backwards to maintain the secrecy.

Implicit in your question is the assumption "if I withdraw my paper I will be able to get it published elsewhere faster".
Are you sure that will happen though? It's entirely possible you withdraw it, send it to another journal, they take six months to review and suggest revisions, and then take another six months to review the revision.
Ultimately it's up to you, but the fact that the editor-in-chief of this journal is responsive is, I think, a good sign that you will get a decision eventually.

It is hard to say. My wife had an article in review for 2 years (top journal in our field) and did get published.
Do not withdraw an article with major revisions but rather the other two.
I recommend you talk with your mentor / advisor - they can hopefully give you the best advice for your career / next steps and what is best.
My wife has had manuscripts rejected only to be accepted by other journals. You need to talk to someone in your field and that knows your situation to provide the best advice.


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Must I hire a proofreader to edit my cover letter and research statement if I'm not a native English speaker?
I am going to apply for a postdoc position in the US. Application requirements include a cover letter and research statement.
I am not a native English speaker and in my department, unfortunately, there is no natives. My question is whether (i) it would be useful/necessary to have both texts checked by a professional copy-editor for grammatical correctness, or (ii) whether I should send them uncorrected.
I understand that '(i)' would facilitate the understanding of the texts. However, '(ii)' would more honestly reflect my level of written English communication.

Are your publications in English? If so, how did you polish them up? How about your advisor? Is there a native-speaker in the department?

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

I have publications in English and Spanish. I polished the English ones (JCR Q1) with the help of professional editors. When editing the post, I indicated that there are no native speakers in my department. Thank you for your response.

There is no reason that you shouldn't have someone else give you advice. But hiring a proof reader might not be necessary. Your advisor can give you advice on content, which is more important, and they or another faculty member might give you advice on the language issues. Your advisor might even give you advice on the question you ask here. If such things are common where you are it is probably harmless.
You need to be able to communicate effectively in the job environment, of course, and will probably have to undergo an interview.
You want your application to be clear and understandable. The worse your writing, the harder it will be for you to break through. Your writing here seems fine, actually, though it is pretty short. Keep it pretty formal, which might be harder or easier, depending on how you learned English.
And, Spanish is the second most used language in the US.

In my opinion, you should not let someone edit your letter. As you said yourself, it "would more honestly reflect my level of written English communication." It is OK that you polish your English publications because you need to explain your research process and conclusions as clear as possible, you present your work in public. But the goal of a cover letter is to introduce yourself, your experience, your goals, why you want to apply for this position. It is about you as a person and researcher, and an editor will remove your individuality, I think so.
If you want to check some grammar moments, spelling, for example, you can install the Grammarly extension to your browser - most of its functions are free. Even if you make some little mistakes, an admission officer knows that you are not a native speaker, so it will be OK.


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How long should I wait to contact an Editor-in-Chief if she told me she would contact soon but has not yet done so?
In another post, I mentioned that I have been waiting for a decision on a revised article for more than 11 months.
During those months of waiting, I have contacted the Editor-in-Chief (EiC) twice to inquire about the article's status, and she has always told me that I would receive her assessment soon. The last time, 1 1/2 months ago, she told me I would receive a response no later than the following week (to date, I have not received any update).
Understanding that EiCs are busy people, I don't know to what extent it would be advisable to email her again now (I fear that my insistence will negatively affect the decision on my article).
Do you think I should contact EiC and send her a friendly reminder, or should I forget it and wait? How long should I wait to write to her again without becoming a pest?

Better not use acronyms that are not generally recognized. Edited.

It is unlikely that badgering an editor is going to speed up the process in any way. In fact, when a lot of people do this, it can just slow it down. Yes, they will probably respond, and their response may just be a way to put you off, but the process is still going to be followed.
The decision may not be an individual decision, actually, and editors may need some sign-off, especially in edge cases.
But whether you keep pushing or not, it will still happen when it happens.
Everybody in your situation is anxious. Relax and move on to the next big thing.


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What can I do if I wrote a grant proposal with a professor, and now that it is funded he refuses to hire me?
I discussed my ideas with a professor at a university here in China, where I live. He said that I should write a grant proposal and he will submit it, and if he gets a grant he will hire me (as a postdoc). So I did write a proposal and finally he got a grant, which will start in September-October. The funds seem to come from this Chinese university.
I do have some written communications in which he stated (or suggested) that he would "hire" me if the grant got funded.
But now he does not want to hire me!
What are my options?
I declined a position because he promised to hire me. Now I have 3 months left in my current position and then I will be unemployed.
He will get the money from this grant with me or without. I just wrote a proposal statement. I am listed in a budget section as a Postdoc fellow and the proposed salary is also listed. My salary is the main part of the budget. It seems to be a good idea for a Prof to kick me from this budget and get a big piece of a pie. (Fortunately, this Prof is not able to get any results from my proposal because he has no idea what I am doing.)
Yesterday, when he said this news, I said that I do not want any explanations. A few hours later I sent him an e-mail where I asked to give me explanations. I have got no answer yet.

it may well be a university rule that it has to go to open competition.

@A.V. Please use this procedure to merge your accounts so that you will be able to edit your post and write comments on it and on the answers.

Would you explain what you mean by he does not want to hire me!? Did he explicitly say that? Yesterday, when he said this news, would you please clarify what the news is about? About he got the grant? Or about he is not going to hire you?

He sad that he will not hire me and I should looking for another job.

There are at least three possible explanations as why the professor told you he was not going to hire you for the up-coming project,

He wants to do it by himself.
He wants to hire somebody else who has similar qualifications and research capabilities to do it with less salary.
He wants to hire you with the salary less than listed on the proposal budget section to do it.

The first possibility is unlikely because he has no idea what you are doing.
The second one and the third one are equally likely. Both are for the reason that he wants a bigger share of the pie. I cannot tell which one is more likely because you did not get his explanation.
If he did not have a candidate to replace you yet, I guess the reason he said he was not going to hire you was an attempt to negotiate the salary. In other words, he wants you to take a pay cut.
I would suggest you to approach him by a face-to-face meeting if you really want to work with him on this project. During the meeting, politely ask him to explain to you why he was not going to hire you for the project. If he ever expresses the desire to cut your salary, then it's up to you whether to accept the offer.
There could be a fourth possibility that he did not want to hire you because the relationship between you is bad. I exclude this one for now because there is no strong indication in your question that this is the case (otherwise he would not ask you to write the proposal in the first place). If indeed the relationship is bad, you'll need to figure out how to repair it if you want to work with him.

In China, does anyone care if you deviate much from your budget?  At least in the US, the NSF does not seem to like this sort of thing and as I recall you're supposed to get permission for significant reallocations of funds.

@Kimball I think reallocation within the fund is possible as long as you have good reasons such as "we didn't anticipate project management would take so much time". Of course, this depends on the agency and the fund manager.

Yes, it seems that he wants to cut my salary. He always complains that he need more money, almost every second he talks about money.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Asking an editor about supplementary files to avoid journal overlength?
Is it OK to write to the editor of a journal requesting that you be allowed to move some parts of the paper to a supplementary file, in order to incorporate the review comments and not exceeding the normal page length? If yes, how do we write such an email?

Some journals allow supplementary material, while others do not.  The first thing to do is to check whether supplementary material is routine for the journal that you are submitting to.  If so, then you may not even need to write to the editor, if your planned use of supplementary material will be like many other papers in the journal.
If supplementary material does not appear to be routine, then it's entirely reasonable to write to the editor handling your paper and ask.  A short and simple query is fine, much along the lines of the question here.  Do this as quickly as possible, however (so that you don't end up in a last-minute panic) and be prepared that you may be told no.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


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Manuscript Revision: Is it alright to include the response to reviewer comments as an attached file rather than typing in the text box provided?
I have recently received a minor revision from a journal. In the manuscript upload portal, there are two places where we could include the response to reviewer comments. One is in the form of a text box and the other in the form of document upload. I am thinking of choosing to include the response file as an attachment as it includes figures and tables that would not be possible to include in the text box. So in the text box I plan to write:

Response to the reviewer comments is included in an attached file (response_to_reviewer comments.doc). We kindly request that you open the document to view the responses.

Is this alright? The journal here is the International Journal of Medical Informatics.

IMHO, if it wasn't, they wouldn't have provided a button for file upload.... Did you check the guidelines for any mention of restriction/format for the file?

@FábioDias No nothing. As per the website https://www.elsevier.com/journals/international-journal-of-medical-informatics/1386-5056/guide-for-authors#21000, it only asks "Regardless of the file format of the original submission, at revision you must provide us with an editable file of the entire article. Keep the layout of the text as simple as possible." There is nothing as such about the response file.

This is perfectly normal in my field (applied mathematics). ASCII text boxes and equations do not mix well, so most of the times people upload a pdf. This happens the majority of the time: referees submit their reviews as pdf, authors answer in a pdf, and no one bats an eye.

@prashanth Then it's even easier. Just attach the file and go on... (I believe you are really overthinking this...)

I'm voting to close this question as off-topic because it depends entirely on the policies of the specific journal. There is no general answer beyond, "Do whatever the journal tells you."

I am very glad to tell that the article got accepted. I uploaded the revision as a separate document and put these in the text box "Response to the reviewer comments is included in an attached file (response_to_reviewer comments.doc). We kindly request to open the document to view the responses."

Speaking as an editor, I don't care whether you put text in the box or upload a separate file as long as what you provide is clear.  Speaking as an author, I have done it both ways many times, and it has never made any difference.  Generally, if the response is relatively short, I'll put it in the box; if the response is long or uses significant formatting (as in your case), I'll attach a file instead and put "See attached comments" in the box.
In short: they wouldn't provide the upload option if they didn't want you to use it.

I'd just prefer to have to deal with one file, not a lot of comments on a webpage and half a dozen attachments.

Personally, I would always use the upload facility to upload a single document and just use the text box to say something like "see attached document for our response to reviewer comments".
There are many reasons why plain ascii text is inadequate. As people have mentioned, if you have figures, tables, or equations, then plain text will not work.
However, even when it is all text, I think that response to reviewer comment documents should have (a) clear headings for each reviewer point, (b) quote the entire reviewer statement, and (c) include quotes of any modifications. All these things are much clearer if different fonts are used for headings, reviewer comments, response text, and quotes of changes. This can be done more easily with a proper uploaded document.


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How to avoid exceeding normal page limits after revision?
I wrote a manuscript that was the maximum length (without any page charges) and sent it to the IEEE Journal of Biomedical and Health Informatics. Now the revisions have come. I am in the process of revising it, but I see that after revision there may be an addition of 1 or 2 pages more. Now for these 1 or pages I have to pay approximately $250 which I don't have. How do I avoid this over-length after incorporating all the revisions?

Are you paying the fee from your own pocket, or charge it to your institution?

I have marked as duplicate even though the linked question is about "before submitted" where this is about "after revision" because I believe that the answers apply equally well to this question.

How do I avoid this over-length after incorporating all the revisions?

There are a few tricks that authors typically use to reduce a manuscript's length (especially for conference papers with hard page limitations), but none would be sufficient to shorten a paper by 1-2 pages, and some of them might be nulled by the copy-editor. Moreover, the changes would be so substantial that the reviewers might require a second round of major revision.
Therefore, if you really can't afford those fees because, e.g., you don't have departmental funds, my suggestion is to ask the publisher if they can waive your overlength fees.


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Citing line numbers of a one-page text in MLA format
Is it considered a valid MLA format for an in-text citation, where a work only has one page, to use the line numbers? Say, (LastName, AuthoredWork 2-3) for instance to cite the quoted lines 2-3 from AuthoredWork by the author? If not, what is the appropriate in-text way to do this for a work with only one page?

A few things:

MLA doesn't require in-text citations to have the author's last name and the title of the article. The format is simply (lastname #pagenumber) or, if the author's last name isn't present, the first thing which occurs in the citation (article title, etc).
MLA also doesn't require line-numbers, nor really allow for it. In text citations are primarily there to help your reader understand the text, and adding line numbers would just prove confusing to readers. Given that it's only 1 page of material, you don't need it either, as the quote will likely be super easy to find for readers.


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What is the meaning of "formalism" in a scientific paper? What is the structure of such paper?
I see some papers that aim to present a formalism for something. First, what probably they are going to do? (for example in the field of computer science) Second, what is the methodology and main structure of such papers (which sections do they need)?

What research field is this referring to?

@eykanal it is in the tags of the question, computer science

As this question seems to be fairly domain-specific, I suggest migrating it to the CS SE site. Also, I would like to mention that term formalism IMHO has several interpretations, including, at least, two science-related: a philosophical one and its mathematical perspective (which the OP is likely interested in).

You seem to be asking many different questions at once. May I suggest that you restrict yourself to the question of what a formalism is and whether what you propose is one?

This question, as far as I understand it, seems very specific to your writing project. I don't think that this site offers the specific tutoring that you are seeking.

As @Wrzlprmft suggested, I make it a general question about formalism

I like to write one, and don't know this type of papers: This is the real problem.  Before attempting to write an academic paper, one has to read a great many existing papers on the same subject, to understand how your work will fit into what is already known.  Once this is done, you will have a much better idea of how issues like this are usually handled.

@NateEldredge I wrote that to say my aim of asking this question, but it doesn't degrade the question. Now I am going to remove this last sentence. You are right, I read a lot, they don't usually say formalism, they say Project, tool, ... but my problem is that technical term for which I like to get help here, otherwise I should read some papers (not related to my work) about formalism

What field of computer science?

@JeffE software engineering or artificial intelligence

"Formalism" is a perfectly ordinary English word, used in its ordinary way. Did you look in a dictionary?

"Formalism" is the practice of using strict and complete methods to define and analyze a model, usually an abstract, idealized model.  Every term is given precise a definition. Every variable, parameter, and factor is given a precise name and definition.  All assumptions are made explicit and are defined precisely.  Qualifiers (e.g. "there exists...", "there does NOT exist...") and quantifiers (e.g. "for any...", "for all...") are made explicit in relational and logical statements.  In formalisms based in logic and mathematics, there are often a set of existential and relational rules called "axioms" that are "given" (assumed to be true), and these axioms are used to prove other existential and relational statements or rules (theorems and lemmas).
It's common and convenient to use symbols and symbol statements rather than words -- i.e. single letters for variables, single shapes for operations, etc.  Depending on the formalism, these could be mathematical and/or logical symbols.
To qualify as a "formalism", the definitions, statements, and rules described above need to be a complete definition of the model and it's mechanisms, ideally with no redundancy or gaps.  Furthermore, a formalism should enable other researchers to reproduce the analysis that leads to the results by following the formalism literally, and without recourse to any other context or information.  While intuition is useful to interpret a formalism and see the value of it in a given context, intuition is never called into the formalism itself.
Finally, a formalism is a world unto itself, in that it's meaning and interpretation do not depend on any connection or any context in the "real world".  Whether or not a formalism has any relevance to real world phenomena is a separate (and important) question.

Regarding paper structure using formalism, the following sections are common after the Introduction:

General description, goals, and scope
Definitions
Assumptions
Axioms
Theorems and proofs
Results
Discussion (i.e. research implications relative to the goals of the model)

In addition, some papers have worked examples to illustrate the model and it's results in particular cases.  I find these very helpful to understand and visualize the model and it's significance.

Thank you! Then if I want to describe a tool and an scheme for a declarative program (like HTML) which is used in the tool to do something, is it called formalism? I guess no

No, it would not be a "formalism".  Describing a software tool, even when done in a complete and exact way, is usually called a "specification", not a formalism.  Likewise for a software program or algorithm.  As @jakebeal said, formalism is just a research tool.  It's useful and appropriate for some purposes, but not all.  If it's not appropriate or useful, don't use it.

It seems to me that you are making a common mistake of classification.  In your question, you speak of a formalism as the goal of a paper.  Instead, I would recommend thinking of formalism as a tool toward achieving some goal.
Since formalism is a tool, and not a goal, it can be presented in a number of different ways, as best serves its position within a larger framework.  To better illustrate this, Let me give a few examples of the use of formalism in a larger narrative from recent papers that I have published:

Formalization used to extract and clarify the "important bits" of a complex model
Formalization used to develop a new set of theoretical guarantees
Formalization user to analyze the tradeoffs between a set of competing approaches
Formalization used to create a predictive model for an experimental system

For each case, the way in which the formalism is best presented varies greatly (although in all cases I like to use certain presentation aids, such as creating a table of symbols).
I would thus recommend starting by asking the following questions:

What is the value of creating this formalism?
What evidence can be presented to demonstrate the value of the formalism?

When you have answered these questions, the arrangement of the formalism within the larger narrative of the paper can follow.

Can I say, by formalism you may mean an arrangement or structure or protocol or grammar for data, components, elements... to achieve something?

@Ahmad Some of these are; others are different types of formalizations.


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What are the industry career prospects for a CS Ph.D. student who doesn't publish in CS?
I am a computer science Ph.D. student, and my advisor is in a different department.  My work is very computational, and kind of CS related, but my advisor mostly wants to publish in journals outside of computer science.  How will that affect my career prospects?  I don't want to be a professor, but it would be nice to secure a good job in industry.
More specifically, I heard that Google/Facebook/other tech companies mostly give the interesting projects to people with Ph.D.s, and give more boring projects to people with bachelor's degrees.  If I have a Ph.D. in CS, but don't really publish in CS conferences, do I still qualify for an interesting project?

What you were told about Google is incorrect.  I worked there for 11 years and disagree that the interesting projects go to people with PhDs.

"Journals outside of computer science". What kind of journals does he prefer then?

@espertus I disagree with your statement.  As a person without a PhD, I interviewed with Google 3 times, and all 3 times they only offered me boring jobs in boring teams.

It's hard to guess whether your work will help you get a job with any particular company, particularly given that you don't say what area you are working in.  In general, however, let me provide an observation about how many companies think about Ph.D.s that may be useful to you.
First, industry typically doesn't care about publications per se.  This is true even for industrial research, just as it would probably be more true for university academia if there were less metric-obsession.  Instead, industry typically is interested in your ability to help meet business goals, and a Ph.D. is typically expected to bring deeper insight and more rarified skills to bear in doing so.
As such, publishing cross-disciplinary research is likely to be an advantage rather than a disadvantage in applying for industrial jobs.  Scientific publication is evidence of your depth, and publishing outside of your "home" discipline is evidence that you are able to reach beyond your intellectual "bubble" and deal with problems of another field as well.

Good points (+1). Completely agree with you on this.


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What order should I list author affiliations on a conference poster?
First and foremost, as the title suggests, in what sort of order should I put author affiliations on the poster? Alphabetical? First author's affiliation, then alphabetical, or some other way (and do excuse me if a similar question has been asked and answered)?

Hi, and welcome to Academia SE! You may want to consider asking your second question about your affiliation in a separate post.

I am taking the liberty of removing your second question, about affiliations, as otherwise your question is in danger of being put on hold.  I believe that you may find the answer your are looking for in this question.  If not, please ask your question about affiliations as a new question.  If you disagree with what I've done, feel free to roll-back the edit.

No problem. I was asking mainly because my own university isn't providing any funding for this while the university I'm doing the fellowship/internship at is paying for everything (housing, food, travel, activities, etc. plus a modest stipend)

I'm not certain that the linked question above answers the 2nd question which was edited out of the post.

Typically, affiliations are listed in the same order as order of authors.
Listing them on a poster should be no different than listing them on a paper or in any other form of scientific communication.
Thus, for example, if you have the following set of authors:

Smith, affiliated with Ivy University
Chou, affiliated with Arrwun Tech
Patel, affiliated with Ivy University
Garcia, affiliated with McName Institute

Then you would typically list them as something like the following (adjusted for your desired format):

Smith, Chou, Patel, and Garcia
Smith and Patel are at Ivy University, Chou is at Arrwun Tech, Garcia is at McName Institute.

As for when authors have multiple affiliations: for any given author, affiliations should be listed in descending order of importance (as judged by the author).  Typically there is a clear "primary" affiliation which comes first, and the order of any others after it matters much less.  The order of the overall set across all authors is determined just the same way as when there are single affiliations, by listing all in order and combining duplicates.


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Should I consider getting an extra degree if I plan to go to graduate school in that field?
I plan to apply to graduate programs in a field unrelated to my current undergraduate studies. Other questions indicate that this is relatively common, but my question is: is there any value in obtaining a degree in my desired field over only taking relevant courses?
I think that having a relevant degree could only be beneficial, but talking with advisors and professors gives me the impression that there is no need to have a relevant degree. Surprisingly to me, there is even some agreement that this could be harmful, since I would require an extra semester to graduate. I'm in no hurry to graduate (currently planning for four years) so I don't quite understand their concerns. Am I missing something entirely?
Do I even need to consider getting the extra degree or is it really unnecessary?

Very closely related question: Graduate school admission with a degree in a different field.

An extra semester is not a long time, so you already have almost all the knowledge you can get as an undergrad to start research. This you could compensate for more efficiently taking a few advanced courses at the master/PhD level specifically targeted to your research.

I have my undergraduate degree in political science and my masters in computer science. Besides having to take all of the required pre-req courses, which added about a year in a half, I never had any issues. The undergraduate for computer science also included a lot of requirements that were useless for my purposes, so it wouldn't have made sense for me to get that degree, then get the Masters. That would have been way more time and money.


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Is it wise (and common) to publish in a peer-reviewed journal without an impact factor to prevent impairement of one's own mean impact factor?
I recently found out that a team of colleagues published in a journal without impact factor, though peer-reviewed. According to my supervisor this happens sometimes when the study cannot be published in a top journal, and then it could be better to do so than publish in a low profile journal whose impact factor would drag down the mean impact factor of the papers published by that team.
Is this common? If so, which elements can specifically drive a research team to choose this option?

Could you write your field? Whether people care about impact factors is somewhat field-dependent. Also, one reason why a journal may not have an impact factor is that it is too new. If a new journal emerges with extremely well-known researchers in the editor board, this indicates the potential for a very high quality of papers in the future. This is a good reason for submitting your own high-quality work there.

This is the first time I've seen the phrase "mean impact factor".  Is this a thing now?

This reasoning is Wrong and Bad in several ways.

First, computing "mean impact factor" for a person or group is insane and should be resisted at all costs.  Even amongst IF-crazy groups, the metric is generally how many high-IF publications have been obtained (ignoring low-IF publications), not the fraction of high-IF publications.
Second, even if you're going to commit yourself to such insanity, the reasonable mathematical interpretation of "no impact factor" is "IF = 0", not "omit from data."  Thus, if you're using this crazy statistic, it should be worse to publish in a no-IF venue.
Finally, a journal with no IF generally falls into one of two categories: either it is good but very new (or just not yet covered by ISI), in which case it will likely have an IF in a couple of years and the strategy will be undone, or else is it complete trash and likely predatory, in which case it will be a worse stain on your record than a moderate-IF publication, even amongst the most IF-crazy communities.

My only possible conclusions are that either:

your supervisor is seriously distorted in their thinking, or
your supervisor is lying to you out of embarrassment to cover the fact that they published (intentionally or accidentally) in a trash/predatory journal.

I would disagree with your #3 - predatory certainly should mean no IF, but no IF for an established journal != predatory. ISI indexing is variable across disciplines, and is not merely dependent on quality - some journals are omitted because of a local geographic focus, for example. Non-English language journals are also strongly underrepresented.

@Andrew Given that ISI has been expanding their scope and retroactively including quality venues that were not previously included (e.g., CS conferences), I would say this still falls into my first fork of point #3: will likely have IF in the future.  I'll edit to clarify.

At least in my field, there are few well-established journals not indexed in WoS. The reason is, they publish mostly non-Englis papers.


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How to select a publishing venue for interdisciplinary research?
I am curious to hear some words of advice on how to select a publishing community for multi-disciplinary topics.
Your contribution is that methods in area A, which is your main area, can solve problems in B more efficiently than traditionally used methods from area C.
Where do you publish, A, B, or C? You are contributing a new application domain to your main area A, along with theory that supports the bridge between A and B, but your reviewers are not familiar with domain B and do not find it relevant. You are contributing new tools to the problem domain B. Finally, all of the related work is in C.
This is CS research, if that helps.

In Bioinformatics there is a classical problem solved with Statistical Mechanics (Physics). I have seen papers on the topic published in all Physics, Bioinformatics, and Biology journals.

Not really an answer (and thus a comment), but have you looked for an appropriate interdisciplinary journal? These do not only exist in the very high ranks (Nature, Science, …). For example, Proc. Roy. Soc. Lond. B says that it “publishes research articles across the mathematical, physical and engineering sciences” (I do not know their stance on computer science though).

The answer of jakebeal seems pretty good to me, but there is another option (to be considered with care, as the line between wise publishing and salami publishing is rather thin): to publish two papers in both A and B. The first paper would describe in depth the technique of the method and could assume knowledge in A; the second paper would assume the conclusion of the first paper (proofs and evidence and technical discussions being there) and would explain how good the method is for the B-problem you are considering, i.e. it would focus on the application of the method. The point of publishing two papers is that community B might have a hard time getting into the technical details of the A-heavy method, while you need to have them documented somewhere.
The first paper might only get published in a lesser venue if community A is not appealed to much by it, but I guess that if community B is excited by your work you might be able to publish the second paper in a first-tier journal or conference. And, as mentioned in a comment, it might be that you have a good starting point for a career in B -- one need not stay in the same field for 40 years, and switching can potentially happen anytime, given the opportunities.

Thank you so much for you suggestion. You are absolutely correct. The methods are too intricate for community B, and that is that worries me about just publishing it in B. I like the idea splitting the paper. A more theoretical paper that justifies the methodology goes to a lower-tier A venue. And then develop an application paper for the community B with a strong real-life application. That is exciting! Thank for your feedback. And it is true, I do like application area B, and I can proceed with both interests.

Where you publish depends on what you are trying to do with a particular publication.  From my own experience with interdisciplinary research, I would say:

Work focusing on the nature of the techniques goes to community A.  These are good for building up your credibility in your home community, building your tenure case in a department of A, etc.
Work focusing on the value and contributions to the application area goes to community B.  These are good for getting your work into use, building collaborations, extending into new areas, building a tenure case in a department of B, et.

If your topic is something that many are thinking about, then there will also likely be some explicitly interdisciplinary AB meetings.  These are often less prestigious than the single-discipline venues, but much better for networking and getting feedback on your work.

I am early in the career, so publishing my area is in my best interest. However, the said paper got rejected twice in the community A conferences because of not high-enough relevance despite very high technical scores. Community B is excited about the work. And there is nothing between A and B. So, do I improve my motivation for community A, or is it time to cut the losses and submit the work to a journal in the application area B?

@afaust Why do you think publishing in Community B is "cutting your losses" if Community A doesn't appreciate your work?  You might find a very nice home in Community B!


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How to get business partner for KTP (innovate UK) application?
I want to know how to get KTP grants. I understand that I need business partner to apply. how to get business partner?
I have read the guidelines for application that it should be with business partner. I do not know how to get business partner to do the work with me.

Can you provide some more information and context?  What field are you working in?  What is your position?  Have you contacted the relevant office at your university to ask for guidance?  Have you got in touch with other people in your field and similar post to ask how they managed it?  Do you already have an idea for what type of business could benefit from your particular expertise?

This is a question about a specific research funding stream in the UK, and strategies for going about applying for and securing funding from this stream would certainly be interesting to many UK early career academics (including myself), so I think it would be on-topic. But I do agree with @FelixU that a lot of context is missing for this to be a well-posed question, especially since not all of the people on this platform are working in UK academia. Might have a stab of improving it in a few hours (if this would be on topic), but can't currently.

Usually, KTP projects are initiated by the business partner, who have a specific need/project in mind that would benefit their company. They then seek a relevant academic partner and apply for KTP funding together.
I'm not sure if you're speaking as an individual or a prospective academic partner. If you're speaking as an individual, you'd expect to just apply for an existing KTP role as advertised on the Innovate UK website/ job search sites.
If you're from a prospective academic partner (i.e. university) with a specific project that would benefit a business in your area of research, do your research into relevant companies, speak to them, and you may find a willing business partner to initiate a KTP bid with.


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Which is important senior (last) author or first author if I have the choice?
I am currently postdoc and I worked on a project of my idea and worked most of it. I do not know should I choose the first author considering that I did most of the work or senior (last )author as it is my idea and will be good thing in future.
I will be corresponding author in both situation

Sorry, but "senior author" is unfamiliar to me. What does it mean? Is it field specific?

Last author, I work in life sciences, usually called this

Isn't that generally the PI? The one that funds the lab?

I am still indecisive  because It is different case scenario, the project is online collaboration that I was responsible for. It was my idea and I had the team. I am also PI.

I will not infrequently be writing a paper and the project PI.  I could easily be first or last author, but would always and without hesitation choose first author.

This won't be flattering to your field, but no reflection on you is implied.
If your field sort of expects that no one in the lab does anything meaningful except the PI and everyone else just basks in the glory, then choose last author. I'd be surprised, however, that you are permitted to do this if you work for a PI.
If your field sort of expects that the PI is always added to the papers from the lab even though they only contribute grant writing and financial support but almost no intellectual content, and that the first author is really the one that does the work, then choose first author.
I actually prefer alphabetical listing, and require that everyone listed actually contribute IP to the paper, but that doesn't always hold sway in the "real" world, and I've deviated from that when it was clear that someone in particular was really driving the ideas, then listing them first. Luckily I was in a field that supports that.
But, unless you know otherwise, I'd guess that first author is more likely to imply the person who is primarily responsible for the work, its direction, and its content.

It is different case scenario, the project is online collaboration that I did. It was my idea and I had the team. It is not PI lab

Still, it is what will pop into the heads of readers when they look at it. What are their assumptions? It can be very field specific as I've surmised from reading a lot of questions here about authorship disputes. Note that those reader assumptions may not be either accurate or rational.


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In the US as a grad student, is it normal to ask a professor for "extra" grant money for doing more research?
I'm currently a grad student in STEM in the US. I'm currently receiving a very modest stipend for acting as a TA, as well as getting credit for some research this semester. I'm also interested in doing some research not directly related to my degree for a professor in my department who has been publishing papers on another, tangentially-related subject.
Would it be normal/acceptable for me to ask for extra pay in return for working on my advisor's pet project, if he would benefit from the work of a research assistant? He's not asking me to anything I'm not getting credit for, I just had the idea that I might ask.
My current stipend isn't making ends meet, and, if I can't get a raise, I'm going to take a part-time job doing menial labor to avoid relying on loans. I don't mind the labor at all but spending the time working on research would be better for my career.

At my university, this would not be permitted because all salaries are set by the department's schedule and not by the professors. My impression is that what you propose is not done. You should also be aware/sensitive that you may not be allowed to take another job if you are technically a state employee (e.g., you are at a state university).

@zeldredge , In the US, I might not be allowed to take another job??? I am a public employee, but I'm not sure whether I work for the state, I will have to look into that before accepting employment elsewhere.
Also, I have received a "research" stipend from another professor over the summer, but I don't get my TA stipend during those months.
My stipend is in fact set by the department, my idea is that I might be able to get an additional income by working to earn a part of the grant money from the research I'd be working on. However it seems that might not be possible.

I don't know the details of such laws, but it's meant to be an anti-corruption measure in general -- to stop people from getting paid by the government for a fake job, I guess. Anyway, just be careful. Your university probably has someone you can ask about this.

Probably your best bet would be to express an interest in a summer research job.  It's okay to be frank about your financial situation.

@aparente001 summer research will pay the bills nine months from now =(

@sig_seg_v - What can I say?  I did not ask for more during the school year.  It wouldn't have felt right -- and the answer probably would have been no.  (I temped during breaks.)

It can be, depending upon the school, the department and their policies.
For instance, I was a PhD student in STEM and received the usual full tuition + insurance + stipend deal that comes with most such offers. This was to be paid out of grant money (RA) or from one of the TA lines depending on the availability of grant money from my adviser that particular semester. I worked on projects that fell at the mutually devised intersection of my adviser and my research interests.
For 1 year though, I worked as an hourly employee for about 5 hours a week extra (a hard limitation since I was an international student in US) for my adviser on one of his pet projects and received the prevailing university rate for a part-time RA (~$15/hour in 2011).
Why don't you ask your adviser?
In addition, I am going to advise that if you are a full time doctoral student and you are receiving a TA but are having a hard time making ends meet, I suggest something like this sub-reddit. Usually, there is a careful calculation by the university to make sure that full time doctoral students get a living wage as a RA/TA.

Whether this is acceptable or not will generally depend on whether the TA and RA are set up as "salaried" positions or as hourly positions, which can vary from institution to institution.

When set up as a salaried position, a TA or RA generally covers tuition and "living expenses," where that living expenses is a stipend intended to be sufficient to enable you to live somewhere nearby in a fairly sparse and monastic manner.  In this case, you are expected to be acting as a full-time student, a significant part of whose time is spoken for by the TA or RA duties.  In this case, it would not be appropriate to ask for a second TA or RA, because you are already being paid for your full expected working time.
When set up as an hourly position, on the other hand, the TA or RA is more of a "piecework" employment, where the school is only paying you for the particular hours you work, and taking no responsibility for ensuring that your pay can cover tuition and living expenses.  In this case, it would be perfectly acceptable to combine this with another job, including another TA or RA.

If you are in the first case and you aren't being able to make ends meet, then you may need to adjust your lifestyle to meet the level of poverty that your institution expects of its students---or else find outside consulting work (if permitted) or organize for better wages.


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Do you believe that all the papers which are published do really deserve to be published?
Have you ever felt that the paper you are reading from a reputable journal did not deserve to be published?

Some people will answer "yes", and other people will answer "no". What's the point of this question?

@ZevChonoles Do you really think anybody will answer yes?  If so, I want to hear them speak!

@jakebeal: I don't understand your question. It appears as if you consider it doubtful that some people will say yes, but in fact you've posted a "yes" answer yourself. Why is it ridiculous for me to have (correctly) predicted that some people would say yes?

@jakebeal: Moreover, my comment simply points out that this question, as written, does not ask for any information further than "yes" or "no" (presumably you wouldn't be interested in hearing a bunch of people speaking if all they said was the word "yes"). There has to be a request for some kind of details, and an explanation of the purpose of gathering this information here on Stack Exchange. Otherwise, I'd say this is clearly "too broad" considering that there is an entire website Retraction Watch devoted to just a specific kind of "undeserving" papers.

@ZevChonoles I meant will anybody answer "Yes, all the papers should be published"

Obviously there exists at least one paper that shouldn't have been published, and there are several reasons why this could happen. E.g. fabricated data, plagiarism, etc.

@Jim Conant: What action(s) should be taken in such cases? or we don't have to do anything as readers?

Additional questions should be asked as questions, not inserted as comments.

@JeffE As noted above, there's an inversion between question and answer, which has caused the "yes" and "no" confusion.  I think we'd all be startled if anybody claimed every published paper really should have been published.

Absolutely, sometimes bad work gets published that shouldn't get published.  To pick one particularly notorious case off the top of my head, consider the case of Jacques Benveniste's "water memory" article in Nature.
Likewise, sometimes good work has a hard time getting published.  To adulterate Churchill's famous quote on democracy: No one pretends that peer review is perfect or all-wise. Indeed, it has been said that peer review is the worst form of determining the truth except all those other forms that have been tried from time to time.

For example: Williamson (2009) Caterpillars evolved from onychophorans by hybridogenesis Proc. Nat. Acad. Sci. USA

My personal favorite is A mathematical model for the determination of total area under glucose tolerance and other metabolic curves, which reinvents the Riemann integral.