text:
Is this what a bad fit means?
I'm 5 months into my 1st data science postdoc and I already feel overwhelmed, intellectually isolated, and now unmotivated. Is this what a bad lab fit means? Let me elaborate below.
I just completed my Phd in CS. The project was heavy on method development with application in Biology. For my postdoc, I wanted to continue this but in a different biology field.
My current lab arrangement is strange. All my team mates are biologists, 1 PI is a MD, the other is data scientist. I've been given lots of small projects to work on while I familiarise myself with the field. Now I'm given yet another dataset, but was told to come up with the biology questions to answer myself. I feel very much out of depth and place but was told I need to show some leadership as I am a postdoc, not an RA. I'm beginning to suspect I'm in the wrong lab, but since I'm new, I also wonder whether this is what a postdoc is all about and that I should stop moaning.
Intellectually isolated. Apart from my data science PI who is also very biology focused, I found myself not able to banter with anyone else about data science/CS ideas or findings. It's like the enthusiasm is no longer there as they're all only interested in biology. Very often, I end up falling back to my PhD team and bantering ideas with them, constantly looking back at the good old days of trading just pure mad ideas or discussing about new discoveries.
Is this a bad fit? Or am I just moaning and being very unfair about the lab? I suspect it's the first and that I need to move on ASAP, but I am not sure to be honest.

I suspect only you can answer. But perhaps one thing to reflect on is whether your bosses are trying to fit a square peg (you) into a round hole. It's possible that they are -- but it's also possible that they are perfectly happy for you to be a square, and they are looking for you to do square research and even set up collaborations with other squares.

Always a pertinent question: Have you talked to your advisers about the issue?

I have, and I was told to show some leadership and come up with the questions since I'm a postdoc not an RA. I was also told that the lab has no infrastructure and resources to support computational method development, and that method development is not data science. This made me very confused. I no longer understand what data science is.

@cag51 it is possible. If that's the case, I'm at a huge disadvantage as I'm inexperienced, operating on a new field, and surrounded by circles not squares. Shouldn't this be better suited for a group leader position rather than a postdoc fresh from phd??

(Not an answer neither an advice): If I were you (and I was), I would continue my work and search at the same time for another position that suits me better (whatever "suits me" means). I would keep a good relationship with the current supervisor.

Yes, it sounds like a bad fit. They were looking for a biologist with some CS creds, and got a computer scientist with interests in biology applications. Both sides are probably unhappy. Not sure what else is there to say about this.

@xLeitix Seems like that should be an answer.

The situation you are describing looks to me like a somewhat clumsy attempt at trying to do multi-/inter-disciplinary research. While your situation is "whole lab working in X while I have background in Y", and the one I have experience with is "a couple of people in X, Y and Z each", the effects seem quite similar -- team/lab members feel intellectually isolated and miss "scientific banter" while questioning whether this environment is helpful for developing their research profile in the direction they want to take it.
The take-away for me is that running interdisciplinary research, projects and teams well is difficult; it's often difficult for people from different fields to communicate efficiently, the projects identified in the cross between the two often seem like "toy problems" to both sides, and it is very difficult for somebody with background in X to pose a hypothesis in Y.
That said, a good postdoc should include a component that is outside of your immediate comfort zone. The skills obtained during your PhD should allow you to get to grips with a different research area. It is an opportunity to widen your horizons and diversify your profile. The perfect ratio of familiar to completely new will vary from person to person, and you need to figure out what yours looks like.
To see whether this is a bad fit, I think you should re-examine your priorities, pros and cons of staying v leaving, and then make the decision accordingly:

Staying
As mentioned, real interdisciplinary research is hard. However it can have far-reaching consequences in one or multiple research fields. If you want to have a interdisciplinary profile, obtaining results from such a project is a very big step in the right direction.
On the other hand, I believe the key to doing this successfully is communication and collaboration. A researcher with a background in X can not be expected to produce a research question in Y. In fact, the hypothesis to look at should come from both X and Y.
If you go down this route, I would suggest trying to establish a new dialogue with your current advisors. You are the authority on CS/DS (that's why they hired you); with very little background in biology. You need to come up with research questions jointly with your advisors, who have a biology background, and a joint plan for dissemination -- you probably want to consider journals they've never heard of, and the other way around too. Pulling off a successful interdisciplinary project must surely count as a show of leadership.

Leaving
If your goal is to find a place to do good interdisciplinary research, well, that's not easy. A number of positions will feel intellectually isolating, and actually feel like "X engineer with applications to Y" rather than "research in X", similar to your current position. The other side of the medal is real research in X, applied to Y, led by somebody from X, which sadly doesn't seem directly relevant to Y to most Y researchers.
It is likely that all interdisciplinary project will likely present a similar challenge to a varying degree (or exactly the opposite problem). Additionally, if you're looking specifically for a marriage between fields X and Y, your options are much more limited than a recent PhD in "just" X.
Finally, it is worth considering whether you actually want to do interdisciplinary research in applications of X to Y. Which aspect of it attracts you the most? If it's just that improving Y has e.g. a direct and beneficial social impact, consider applying X to any field of high social importance. If it is that Y just provided interesting challenges, consider continuing doing research in X, unbounded. But if it is Y specifically, you might need to get background knowledge in an area different to your current background even if it means stepping far out of your comfort zone.

I think your boss expects you to use new data to generate testable hypotheses. After all, data science is a tool. That said, I am a bit puzzled as to why you chose this academic lab instead of industrial postdoc in any of the three public cloud companies. But I think your motivation for coming to this lab is that you want to use data science to contribute to biological science.
I can’t tell you if this is a bad fit as you described, but I think the questions for you to consider are: are you able to use data to create hypotheses? Does the data indicate things or evidence that doesn’t fit conventional wisdom? What experiment (ie, knock out genes, ligand binding site mutation) can you propose to validate your hypotheses? Can you build a classifier or tree from data to categorize these observations? And does the tree recapitulate or defy known  biological principles? These may yield valuable research topics (speaking bluntly, grant proposal). I think these are what your boss is expecting you do deliver.

I am a bit puzzled as to why you chose this academic lab instead of industrial postdoc in any of the three public cloud companies - Sorry, where is this coming from?

Academia labs are not the only place to do peer reviewed research. For those who thinks academia is not their gig, there are industry options.

For those who thinks academia is not their gig, there are industry options - Sure, but I didn't see anything in their post suggesting the OP thinks academia is not for them, and especially not suggesting that they felt this way when they were applying for jobs.

Well, it looks like they wanted someone to do their data science for them and are expecting you to make yourself useful. That is, to solve biology problems with data science: what else is data science for if not for solving problems in various fields?
You, on the other hand, seem to want to discuss the data science itself, compare approaches, examine properties of data... And it seems that you would not find it in this lab indeed.
I would say I have not seen this arrangement anywhere except for CS/ML labs which act as a workshop for an entire department or even university, and they often deal with a huge range of problems, sometimes from social sciences to geology. Industry has more specialized ML-focused groups, but in natural sciences within academia, ML is not yet seen as something warranting dedicating an entire subfield or a lab to. In part it is because the interpretable AI is still rather weak, and without it, data science usage is limited to methodological aspects. To put it bluntly, it is "just" advanced statistics, and you do not need a dedicated Lab of Pearson Type VI Distributions in Plant Biology: instead, you have a Plant Biology lab which brings their statistical problems to statisticians.
If you want to do data science with applications in X, two main options exist: you either join a lab specializing in X as a specialist in data science and largely handle data science problems solo (which is the situation you are in right now; I am in a similar arrangement, but content with it) or you join a data science lab and pester labs in field X for collaboration. The latter option seems to fit your profile better.

Eh, I'd push back a bit against the "in natural sciences within academia, ML is not yet seen as something warranting dedicating an entire subfield or a lab to" bits; there is a lot of heterogeneity in how biologists view the utility of ML and AI, and also "not yet seen as" sounds like in some future you're imagining every biology lab is going to have a sub-lab to do AI. I think that's rather silly; biologists use tools from all sorts of disciplines, and they need people familiar with using those tools, but that doesn't mean it makes any sense at all to also have people developing new tools.

The people working on new tools are naturally going to be in groups that work on new tools. Typically, if a biology lab has need for a particular new tool, they're going to work in collaboration with some other lab that has expertise in that tool, whether that tool is a piece of analytical equipment (collaborating with physicists, chemists, engineers, etc) or data analysis (statisticians, computer scientists, bioinformaticians, etc).

@BryanKrause Thank you for your comment; I seemingly have failed to make it clear. Yes, I am much with you on "the people working on new tools are naturally going to be in groups that work on new tools". The caveat here is that it is not always the case, and I've seen quite a few labs with homebrew solutions for something someone else knows how to do better. As for the "in some future you're imagining..." - I do think that it is possible that in some, not all, areas there will be labs heavily specializing on these tools in some subfield of biology. I'd argue some genomics labs are almost that.

But yes, a TL;DR would be "if you are interested in tools way more than biology, you need a tools lab, not a biology lab".

Sure, certainly; there is an entire field of bioinformatics that lies on the intersection of computer science, statistics, and biology, but that's a fairly narrow slice of biology in general and even in bioinformatics most groups are using existing tools rather than making their own, just like field biologists tend to buy binoculars and notebooks rather than making their own optics and paper.

Thank you for the insight folks. I must admit, I came to the lab with the view of solving biological problems with data science. However, I did not expect to be told to go hunting those biological problems myself, which is what biology focus groups are in general. I came from a CS lab with collaboration with biology lab. The latter came up with a problem, we came up with the solution to solve the problem, and I think that's where I want to end up.

@BryanKrause the field exists but is only appreciated in some parts of the world. I think labs operating in that area are very concentrated in some part of Western Europe and US, with some scattered in much smaller scale elsewhere. These labs tend to be headed by a statistician or CS guru who have interest in solving biology problems rather than say facial recognition or database management (both are classic CS stuff).

All of these conversation reminds me of what the MD PI said "I hire people for their expertise. As you can see, each lab member around you is an expert in a field or sub-field". We are a diverse group composed of a person who is either an immunologist, a wet-lab tech expert (idk what to call this person), a gene regulatory network expert, a gene mutation expert, all within a biology group trying to study a disease. I guess, these guys are all an expert in a biology field, while I'm more of a ML/data expert in CS field.

I have seen people who have been "scientific outsiders" in their labs or work environments in the sense that their interest and expertise was in some way only loosely related to what the others do. Sometimes this kind of thing is required because a lab may need this kind of expertise occasionally, but most if not all people there can't really relate to it.
Now you can say that this is a "bad fit" and look for something else, but I have seen people who have managed to "cultivate" such a position in some often creative ways. This usually involves contacts to people working elsewhere (surely at least to avoid intellectual isolation) who may be closer to what you want to do. Chances are as a postdoc of whom personal initiative is expected, you can well work on collaborative projects with people who do not belong to the lab. This may comprise people who develop ML methods, or people who provide you with biological problems that you can contribute to. Obviously the first candidates would be those you already know from past experiences, but you may get into contact with other people doing stuff of which you have an idea what you could contribute.
I also wonder whether you could just interpret the "show some leadership" demand as a license to do what you're good at. Would it be a problem if you focus more on methodological work, as long as you can make an at least weak case that there are biological problems where this can be applied? Maybe you need to look around a bit for such problems, and maybe with some creativity you can connect this to the data set that you are apparently expected to do something about.
One thing that I recommend strongly is to collect some information about what "counts" for your lab, like publications in specific journals, grants etc. In many places you have a lot of freedom if you just produce something that counts. You could maybe spend 80% of your time on projects that you have chosen more or less freely for yourself as long as you contribute to the lab's output in a way that serves the lab. (Chances are it won't be like that everywhere, you've got to find it out.)


text:
Designing a Teaching Innovation Study for Slow Learners in Civil Engineering
I am an Assistant Professor of Civil Engineering. I have recently been tasked by the Department Chair to design a teaching innovation study with the focus to support and enhance the academic performance of slow learners, specifically targeting students with a CGPA of 5 to 7 on a 10-point scale.
I don't have any prior experience in designing a study of pedagogical nature, I am reaching out for advice and pointers on how to approach this.
Are there any resources, such as books, articles, or websites that you would recommend for someone new to designing educational studies? Any insights, experiences, or resources would be incredibly helpful.
I've searched for articles using keywords like 'slow learners', but most of the literature I found focuses on elementary school students or non-engineering courses.

sounds like an worth while project, but your question is a shopping question and off topic for this site. Perhaps try looking for "Engineering education research" (e.g., https://en.wikipedia.org/wiki/Engineering_education_research) or "engineering pedagogical research" to refine your search.

This is a resource question, not a shopping question @RichardErickson.

Search for "Pedagogical Patterns". There is a lot of activity in that community, directed at effective teaching in general, but mostly in STEM education.

What is the purpose of your "study"? Is it simply to understand slow learners or do you really want to find and implement effective pedagogy?

Being a bit suspicious by this point in my life, this sounds like some sort of trap, with intentional or not...

Are they actually slow learners vs unmotivated vs juggling too many courses vs who knows what??? The approach would likely be different for these and other scenarios.

@Buffy we want to find and implement pedagogy for slow learners, implement for two semesters and monitor changes in academic performance

@JonCuster They are slow learners with low motivation. They do not have any more courses than other students in their class.

@user3024069 - so you have declared them as such and will stick by your label. And, should they not respond to your attempt, what will you call them next? Teaching is hard, people learn in many different ways for many different reasons. Perhaps redesigning the original courses to benefit a broader range of learning styles would be the first step.

Contact the education department in your university, or perhaps the teaching excellence center. If you have no background in designing studies and interventions, you will do about as good a job as if someone suggested you do a study of old English history.
In other words, get in contact with the experts and ask for their help. Perhaps even ask your department head to make this connection for you.

There is no education department or teaching center. That's why I'm struggling

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

sort: votes


text:
In the UK, who owns the intellectual property of a thesis?
Assume the following problem:
A person decides to create software for his thesis. His application turns out to be very profitable.
If he continues creating it, will the University own the intellectual property over the thesis or the application itself?
Will the revenue go to the university instead?
Is there any way the two parties can come up with a contract or agreement?
If the person leaves university and doesn't finish his thesis and instead releases his application, will there be any repercussions?

It seems like a legal question, perhaps on-topic on law.SE?

Usually anything created as part of your studies belongs to the University, see your contract with them. Read it with a lawyer to be sure.

Thanks. I added law as a tag.

Since you already have [tag:legal-issues] is swapped it for [tag:united-kingdom]. It is specific to UK

Depends on the University. The university (in the UK) I most recently worked at had an Intellectual Property policy that all IP rights for students stayed with the student automatically, which differed from the policy for research staff. But the university would be happy to get involved to help commercialise in return for a share, much as your suggestion about an agreement. However, other universities have other IP policies. But whatever their policy is, it should be easily available from their intranet though it might not be available to people outside the institution.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Asking letter of reccomendation to a Professor I've had this semester
I want to be admitted to a European program that would mean so much to my future carreer. Particularly important documents to be sent with the application are reccomendation letters from professors. I already asked my Bachelor advisor and he told me he will write the letter for me, and that's great. But in the call for this program it is specified that up to 3 letters may be sent, and of course I want to exploit this possibility. I'd like to ask the letter to one of my professors of this semester (I'm attending the Master degree). He taught me two subjects; I've already taken a midterm of one of the subjects and got the maximum grade. I always attend lectures and I guess the professor noticed my interest in his subjects since I often ask questions or reply to the questions he poses to us during the lectures. Is it inappropriate to ask him a reccomendation letter if he's only known me this semester and we don't have a particular relationship (e.g. student-advisor)? He is very well known internationally and I think this letter could boost up my application to the program I want to participate to.

If you have had enough interactions that he can judge your potential, then he will probably be willing to write a letter - time permitting. But you can also ask him if he has enough confidence in you to write a letter. I strongly recommend that if you ask, you do so in person, rather than by email. He will probably need to know a bit more about you to be comfortable after only knowing you for a short time.
But nothing you say indicates he would be a poor choice.


text:
Is a request to publish an article in Research Features a scam?
I regularly receive emails from Open Access predatory journals or conferences asking me to publish an article or attend some kind of conference somewhere. Usually, those emails are easy to identify.
Recently, I received an email from a Journal called Research Features, inviting me to publish an article in their journal which focuses more on outreach if I understand them correctly.
Does anybody have any experience with this (or a similar) journal, is this a serious thing?

A general rule of thumb based on my experience: if you are not sure if a  journal/conference is predatory, then it is almost certainly predatory.

Be super careful when tapping on these links. These could be phising links taking you to a phising site that looks legit. Your device could get compromised before you even know it. If you can, copy the link, log out of your email, open a new private window, paste the link and view them there.

Also, if you have spare time, you can do a quick malware check on the links online to see if the links are malicious or not.

Another rule of thumb: If they ask you without any prior contact, it is probably a scam. Usually you need to contact the journal and not vice versa.

For anyone reading this question, they seem to have a launched a twin site called Research Outreach. Same model (you have to pay them to publish), same scam.

This is an interesting thread as I am one of you who got an email from this magazine. My first goal was to identify the nature of this magazine and if it is of any worth. I think this thread has answered most of the questions that were popping up in my head. I think I would simply ignore their email this time. :) Have a good day everyone! Cheers,

Research Features is a UK-based magazine intended for a broad audience (outreach), it is not a peer-reviewed academic journal.
So in one sense it is legitimate: it's a real magazine with real contributors that some people genuinely read. You can contribute a piece if you so wish to.
I do not think it claims to be a journal.

"We are not a scholarly publisher. We sit somewhere in the middle and
  feel very comfortable in our unique space. We will never engage in
  ‘click-bait’ or ‘tabloid’ pop-science; but we do not offer complex
  peer-reviewed content. Our publication offers detailed insight using
  clear language and a visual format which translates complex science,
  whilst remaining respectful."

Source: https://researchfeatures.com/about/

The link is to Research Features and as far as I can tell there is no such journal as Research Futures.  I think this is clearly just a typo in this answer.

@scaaahu that must have been a typo (which I did not recognized), thank you Peter K. for correcting it

I have some experience with writing to outreach magazines (which I would label this). It can be quite rewarding to present research to a broader audience, but also demanding. Two pieces of advise:
1) Ask if you will have an editorial assistant associated. They can do wonders for your writing, and offer good journalistic insight.
2) Require appropriate monetary compensation.

Research Outreach asks the writer for paiement, not the reverse!

I think there are two clearly distinct models - nabla is thinking of magazines where the author writes the article and gets paid, while Xi'an (and OP) talk about magazines where the author pays a science journalist to write the article about the scientists work. Both can in my opinion be valid, and appeal to different scientists. If you have the time and skills to write a great public piece about  your work there is little reason to pay somebody else to do it, but this will simply not be true for most scientists.

I got contacted by Research Features twice. Yes it's true they want you to pay for using your research. If that's enough to call them "predatory", they are. However, this is not about just publishing your work. It's not an academic journal. This is about making more visible work that you have already published, something that you probably can't easily do yourself just sending to another journal. They do some service, i.e., rewriting with a broad audience in mind, advertising, etc. They are upfront about payments, and for the money they promise to do some proper work. They also asked me for a personal discussion. I have instead asked them to tell me in written form what they offer. They ask for between 1500 and 2000 GBP and have sent a detailed list of their services.
I have not taken up their offer, however I don't have an issue with it. If they indeed do what they promise to do (which I haven't checked), I have seen worse things to spend my money on. Offering a service of this kind and asking to be paid for it is legitimate in my view. Whether the service is good and will be worthwhile for you is another question of course.

Okay, so adding an updated answer based on their recent contact with me.
They sent me multiple emails (5-6) at different times, after reading the answers I thought about giving it a try and replying to them ("my initial assumption was if it's free, then why not just give my less academic style articles to them [the contact person tried to convince me initially it would be free and will take very low amount of time]")
After I replied, he insisted on a call, but eventually, I tried to get the catch. It turns out, they will charge you £1950 per article, which was not mentioned initially.
They also include "The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without the written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future.
To ensure we do not email you again, please reply to this email with the word ‘remove’ in the subject title and we shall erase all your details from our system. Thank you." in their emails so that no one can share the email content I guess. They sound kind of professional.
But, yeah, it's a full-on scam to me. With that fee, you can probably submit to a good-quality peer-reviewed journal.
Don't reply to avoid wasting your time.
Their service page with pricing: https://researchfeatures.com/services/

They share the same street address and web styling as another similar magazine, Research Outreach:
https://researchoutreach.org/our-company/
Same people, same idea, similar content (though I have not checked for overlaps).
I might give this one a miss.

They also charge you for the content you create and give them for free.

It's predatory for me. You can browse their latest issues, for example this one, all are from Asian academics. I am Asian and the article they mentioned and invited me for was published years ago and they said

we understand your work is still going..

Looks like one has to pay; at least invitiation mail says "the cost for taking part" so: rather scammy

I just received an email from them and I found this rather appalling and fishy:

Rather than writing any further detail, could we find a few moments to
discuss over the phone or Zoom?
Before we take an introductory call, could you please take a few
moments to look over our website and gain an understanding of how we
work.
I can then answer all your questions regarding our process, the cost
for taking part, methods, and the different solutions we offer.

So, I decided not to contact them at all.

authors: Xi'an ні війні


text:
Does adding an MIT-licenced package to my research software qualify the author for co-authorship?
I have a research software on GitHub, using an MIT license. I need to include an additional package/library, which is also MIT-licensed, to my software for a new feature to work properly. I do not know the author of that package personally, I just found it online (also on GitHub).
My question now: If I publish my research software in the near future to a platform like Zenodo or something else where I get a DOI, would I include the author of that additional package as a co-author?
My initial guess was no, but instead cite his package/library and thus include it in a list of references. But maybe the research software experts here have a different, more elaborated view on this.

Reminder to please avoid writing answers in the comments.

No, absolutely not.
Credit the author for what you have used of theirs with a citation and clear statement of what you used. That covers you from an academic ethics and plagiarism perspective.
Then, also make sure you comply with the terms of the license when distributing your software. That covers you from a software license perspective. MIT is quite permissive but you still need to comply with the terms.

... and this is not much different from using other people's work in other forms and other ways. The discoveries they've made, the instruments they've designed or built, the materials they've prepared -- if these have special importance in your own work then they certainly should be acknowledged appropriately, but that you rely on such works does not, itself, make the people who made them participants in your own work.

I agree. It is only if you have engaged with the developer and discussed your research, and through collaboration they extended the software or otherwise personally guided you how to use the software to answer your research question that you would consider co-authorship.


text:
what are my options if the degree i want is not available on my country?
Hello this is the first time i post something here:
I live in Argentina and I'm 18. Currently, I'm giving my evaluation exams to enter UTN university (It's one of the best universities in Argentina, it's public).
I wanted to study software engineering but that is a rare degree in Argentina, however i found a private university (Not as good as the public ones) but i don't have any reference of it. So i don't know if it is going to be worthy studying 5 or more years there at all.
The actual problem is that in UTN i'm studying systems engineering, is the closest degree i know it's going to be worthy but i don't want a systems engineering job in the future. (Although i know people who has a Systems E degree and works as a software E instead).
So i don't know what to do. I wouldn't mind move to another country, the problem is i really have no idea of what to do then, i can't move to another country but not knowing for sure if i was accepted by the university or not!
Also i don't know another's country's universities.
I only speak Spanish and English, but does anybody have an idea of a country exchange or something that asures me i that i have been accepted in university, so then i can move to that country to study?.

What about doing a bachelor in systems engineering at UTN and then doing a master more close to what you really want in another country? Several universities in Europe offer master programs in English.

Yes but what would be the point of doing that? I can directly go to the university. "Several universities in Europe offer master programs in English." I will look into it. Thanks @FuzzyLeapfrog

Most bachelor programs are in the language of the country. That would be the point of doing this. Additionally, you could learn the language of the country where you want to do your master to enhance your chances.

From your question, it seems like there is a misunderstanding about the process of studying abroad:
If you want to study abroad, you first apply for admission (and possibly scholarships). Only if you are accepted (and you accept the offer), you start your preparations to move to the place of study. There is no need to move before having been accepted.
You also don't need an exchange program between countries in order to do that. You just apply to a university that you are interested in, using the documentation of your previous studies that you have (e.g., high school degree). Applications from abroad are quite normal in many institutions.
On a related note: for most countries in the world, in order to study there, you need a proper visa. You will only be able to get a visa that allows you to study there after you have been accepted for a program.
As to finding out where you should apply to: this is the more difficult question, as this is quite subjective. There are university rankings that give you an idea of what very good universities are out there. Note that these rankings have their own problems, but they are often a start. Then, you can search for research papers in some sub-area of software engineering that you find interesting. If you find very strong research groups in that area, you may want to find out about the courses of study being offered at their institution.

Pick a software engineering program at a U.S. university and carefully examine the degree program (i.e. what courses are required, which courses are prerequisites for which other courses).  Then carefully read the course descriptions.  Preview online the textbooks required for each course.
Now compare all that with the degree program for systems engineering at UTN to find out how much overlap there is.

Interview a couple of people in your area who work in software engineering.  Find out what coursework and training they found most helpful.

It is often easier to seek admission abroad after finishing a Bachelor's degree.

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


text:
Revised manuscript for a long time
We have submitted a review to high-impact factor journal in Elsevier, and after 15 days only, the reviewing process has ended with major revision. We addressed the suggested point carefully and the revised manuscript has been re-submitted. The status has returned back to under review and for 1 month no update on the status.
Is it common for the revised manuscript to take longer time than the original one?


text:
How long after DFG grant to start work
One way in Germany to get money for academic research is to apply for grants at the German Research Foundation called DFG. The DFG provides information on numerous things through documents. If you apply for your own position as a temporary principal investigator Eigene Stelle, the review process takes around 6 to 7 months.
What I was not able to find any information on was how long it takes to start work after you got a DFG grant. If the DFG tells me on 01.01. that I got the grant, how long would it take until I can start work and get paid from that grant?
This
How do the logistics work for recipients of a DFG "Eigene Stelle" grant (in Germany)?
describes some of the technicalities after you get a grant, but does not mention anything about how long all that takes.

Just one piece of advice: Give the DFG a call. Your contact person should be mentioned in the letter that you got the grant. They will be able to answer this question and any other question you may have instantaneously. The DFG contact persons are usually very supportive.

@Snijderfrey I don't get the sense that OP actually has gotten a grant like this, but are intending to plan ahead; this is quite important if one is trying to be funded continuously without gaps.

@BryanKrause, you might be right. BureucracyIsAWasteOfTime, would you clarify?

I think the bottleneck isn't the DFG but the host Institution. They might need a few weeks to prepare your employment contract(s) etc.

At my university in Germany they are so understaffed in the human resources department that it can take not weeks but months at the moment to get someone employed.

I have got a DFG grant application in process, but depending on how long it takes between the DFG telling me I got or did not get it and actually working, I would now apply for something. If it is just a few weeks, I do not have to apply for anything else. If it is a few months, an application somewhere is advisable.

@BureucracyIsAWasteOfTime What will you do if your application is not successful?

I do not compute. I did not even know those words could be used like this in a sentence. I have a non academic job I can always do, but that is not ideal. Additionally there is a 6 month academic position I was advised to apply for, where the application is mostly a formality, but it is not well funded. The DFG should inform me soon about the grant. Consequently, I have to decide soon whether to apply for that position or not. If I already know now that it takes months to actually start work, I'd probably take that 6 month position. If it only takes weeks, there is no need.


text:
How should a teaching assistant explain his absence to the course instructor?
As an international TA getting accustomed to the landscape of my University, I managed to earn the ire of my instructor/professor for having not shown up during the discussion/office hours.
In a strongly worded mail, he has sought an explanation while reprimanding me saying that another instance of this would lead to serious consequences.
I am afraid that I may lose my assistantship as I curse my folly for being so careless. I have apologized to the Professor over mail but from the tone of his reply, he seems to have not considered it. Please suggest how I must handle this predicament.

Honestly. How else?

And avoid silly excuses like "As an international TA getting accustomed to the landscape of my University". Being international has nothing to do for you not showing up to work you are paid to do.

@Alexandros: Well, that depends - to me, at least from reading this question, it isn't at all obvious that a TA should be present during "discussion/office hours". While there is no real distinction between RAs and TAs in my place, and rather, everyone does some research and some teaching, whenever I co-organized a lecture, I was never required to be present during the professor's office hours (or even the lecture itself, for that matter). The OP should clarify whether this requirement of being present was clearly laid out to them, e.g. in their work contract.

If your writing style is usually as in this question, and if you would have written in like manner to me, expressions such as "earn the ire", "the landscape of my university", and "I curse my folly" would have made me feel mocked instead of receiving an apology, or at least as dealing with someone who is impossible to get through to.

@gnometorule: I doubt that helps the case you are concerned about in any way, but for precision's sake, please note that "earn the ire" was edited into the question by "Community" in order to replace "vent the irk".

@O.R.Mapper: Thanks for pointing this out!. "Vent the irk" - again, to my ears - is even stronger support for what I feel about the style, and what others might too. It's a 6 sigma expression at best.

"getting accustomed to the landscape of my University" is the biggest BS excuse I have seen in ages. And BS here does not mean Bachelor of Science.

@QuoraFeans: I think it is appreciated on this site to provide some rationale for one's stance, with or without reinforcement by acronyms that do not mean "Bachelor of Science". While I would agree that "getting accustomed to the landscape of my University" is an unnecessarily "poetic" way of expressing a simple fact, being unfamiliar with unwritten and non-self-explaining rules of a foreign place seems like a pretty valid excuse to me, as I've explained in my comment above.

@O.R.Mapper: the OP does not claim he didn't know the rules, but he didn't know "the landscape of the University." That implies that he wanted to attend, but could not find his department.

@QuoraFeans: Ooh ... I (and maybe others here?) interpreted that in a far more figurative sense: I took the "landscape" to mean the general network and structure of dependencies, connections, and processes in the organization of the university as the OP's new social environment, not literally the geographical topology of the physical campus. (Not saying that is the intended interpretation; it just seemed the most straightforward and obvious one to me. The possibility that "landscape" might be meant in the literal sense didn't come to my mind.) The OP should clarify what was actually meant.

@O.R.Mapper: yes, there is a need for clarification. Anyway, maybe I should assume good faith, and construe the sentence more benignly. However, given the irate answer of his prof, I suppose this was not a  slip where we can assume an honest mistake.

This doesn't appear to have much to do with academia. It's just a question about basic human interaction, isn't it? Essentially, "how do I apologise for missing an appointment"?

@LightnessRacesinOrbit - Conceptually yes, I think, but the OP framed the question from the perspective of "I am an international student afraid of losing my TA position."  While one could argue that this is no different than another job, the fact that it's a question about interacting with people in academia while holding a job in academia gives it enough reason to be here in my mind.

The best way to handle this is to acknowledge that you've screwed up, and to explain how you're going to make sure that you won't miss any class meetings and other events in the future. If there's a justification for why you missed the event (for instance, if you had an examination for a class you were enrolled in overlapping with office hours), you can mention that.

+1 for "explain how you're going to make sure that you won't miss any class meetings and other events in the future".

+1. Explain how you'll do better, not just explain that you'll do better.

I second the other advice given here, and in addition I recommend that you make your apology in person rather than by e-mail if you have a chance.
I have been in this situation before, as the professor. I was pretty upset at first, but once I met with the TA he sincerely apologized, explained why it happened without trying to excuse his behavior, and said the mistake wouldn't be repeated. Within two minutes I was no longer angry at all.

In-person explanations appeased two out of two of my college professors for my newborn-baby-fatigue-induced-shenanigans as a GTA (of which there were two, one per professor). And two out of two of those explanations did not use newborn-baby-fatigue-induced excuses. The apologies were abject, with a promise that the mistake wouldn't be repeated, and the following discussions were unrelated, interesting, and relationship-enhancing. And I should add that even today I know there was no good excuse, and I was an idiot. They were both my friends afterward, and told others I was a decent instructor.

Please suggest how I must handle this predicament.

Apologize, and don't do it again.

. . . . Spot on.

What information had you received prior to the discussion/office hours that informed you that you had to be there?
If the answer is none then stand your ground: "I'm regret that discussion session was compromised by my absence however I never received any information indicating I should be present. The only relevant communications I've received were the e-mails from W dated X, Y and Z, none of which indicated that my presence was expected at these discussion sessions. Now that I know that I am expected to attend I will be present at all future sessions."
If the answer if you had the information and failed to act on it then apologise and make sure it doesn't happen again: "I am very sorry not to have attended the discussion session, this was entirely my own error and I will make sure it never happens again."
The most important thing is simply to be reliable in future.

"The only relevant communications I've received ... none of which indicated that my presence was expected." That's a dangerous line to take, unless you are 100% certain the statement "All TAs are expected to attend office hours" is not hidden on page 293 of some admin document that you should have read in full before you agreed to it by becoming a TA. A simple "I was not aware that I was required to attend" is (presumably) a factual statement, and less confrontational.

If you did not have the information (ie were not told),
a alternative line to "I did not receive any communication informing me I was expected to be there." is "I'm sorry, I must have skip over the message that told me it to be there." that way you are absorbing the blame yourself, rather than suggesting someone else failed. Even if someone else screwed up, you come out better by just taking on all the blame yourself (even if unfairly).

Years I developed a framework for the ideal apology -

Say you are sorry.
Acknowledge that it was your fault.
Acknowledge that you impacted or hurt the other person and they are right to be angry with you.
Promise the action will not be repeated.

What's purposely missing from the above is an excuse. I suppose if a parent passes away, it might slip your mind to contact your appointments, but even so, as a general set of rules, avoid excuses.

The first thing to do would be to accept and apologise as suggested by @aeismail. Then you should probably make up for it by doing some more work the next week or making a pleasing amount of progress in your research and produce the outcomes to your professor.

For the time being, do whatever it takes in order that you do not get sacked. Technical advice for that has already been given.
If it is indeed true that the instructor already rejected a reasonable apology from you, then work on an exit strategy from the employment relationship with that instructor. I always demand reliability and meticulousness from those whom I work with. However, mistakes happen, and when they do, it is important to limit the damage and then move on quickly. There is no need to humiliate anyone for making a mistake, like demanding multiple apologies. (If mistakes by the same person accumulate, the situation changes. But this seems not to be the case here.)

"exit strategy from that group"  You mean, don't TA for the same professor again?  It doesn't sound like there is any connection with the research group (question says "course instructor", not "advisor" or "supervisor")

I downvoted because I don't see that the professor has behaved unreasonably, or demanded multiple apologies. When I have TAs working for me in a course, part of their responsibilities are to hold office hours (on their own; I have my own office hours in my own office). If I heard from students that they had shown up to the TA's office hours to find that the TA was absent, the first step would be a strongly-worded e-mail making clear that their funding depended on doing their job. If their response didn't indicate they understood the seriousness of what happened, I would continue to be worried.

@Tom: my advice was based on this part of the question: "I have apologized to the Professor over mail but from the tone of his reply, he seems to have not considered it." I have changed the wording of my answer to: "If it is indeed true, ..."

@TomChurch: "When I have TAs working for me in a course, part of their responsibilities are to hold office hours" - it hasn't even been established yet whether this applies so generally to the OP alike, and whether they were aware of that duty. As such, I think we lack some crucial information to evaluate whether this answer does or does not make sense in the given context.

@O.R.Mapper This answer makes sense in an industry work environment. There,  you work on an exit strategy from the employment relationship when you have an unreasonable boss. I am not too sure a TA would do that just because he worked for an unreasonable instructor. After all, a TA is a part tim job and the OP is most likely an international graduate student.

@scaaahu: Especially because it's just a part-time job at the university, I don't see why it would be unreasonable to find a different TA job the next semester if you don't like the instructor of the current one. Unlike it is the case with an industry job, it's probably not even a question of possibly moving to another city, the "exit strategy" is to check openings from other departments on the same campus. But anyway, my comment on whether or not the answer makes any sense was focused on the fact that we don't yet know whether the instructor was indeed unreasonable.

@O.R.Mapper The way I understand how it works in industry when you find a different job is much easier than finding a TA job in Academia. If I understand it correctly, the department assigns TAs to professorss. A TA hardly has much to say when change a professor he works for. Maybe I am wrong about this. Please correct me if you will?

@scaaahu: Maybe that's the case in some places. In my country, students look for "student research assistant" (that can be TA or RA, or both) job postings on department websites and on the campus, and then send an application to whoever is indicated as the contact person (usually a professor, post-doc, or a doctoral candidate, who wants to outsource some of their work), who may or may not invite them for an interview, depending on which a decision on whether to employ that student will be made. I was not aware some universities do not let students choose who they work for.

@O.R.Mapper I understand it now. Maybe the OP of this answer comes from similar environment as yours. Thanks for the info.

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


text:
Online/Distance Math Teaching
I am a math instructor at local community college. I am in mid 60's and in good health except for a minor mobility issue. Teaching is mentally very rewarding. Beside teaching, I am also tutoring students on Calculus by Skype in my spare times. In fact, I have a corner my home converted to a mini studio complete with big whiteboard, HD camera, special lighting, etc. Although I have only a few students right now but they all express great satisfaction with my distance tutoring for its convenience and flexibility.
In my thought of thoughts, I used to muse that, wouldn't it be great if I am able to work as adjunct online math instructor, such that I may still have a rewarding activity in my retirement years when my mobility issue become a major issue? I would like to make small baby-steps one at a time. But I do not have any distance teaching experience. I have been trying to gain a foothold in this online craft by applying to small part-time online teaching position but without success. Here are my two questions:
(1) Is there any prep that I can do right now to improve chance of getting hired in the future? Certification perhaps, but what certification? Maybe volunteering at a non-profit institution, but where?
(2) My understanding is that almost all online classes are either on BlackBoard or Moodle platform. Does this mean that my experience with Skype distance teaching is irrelevant when applying online position?
I would appreciate any help or suggestion from you. Thank you very much for you time.

The SUNY system has a huge number of online classes.  Some of them are excellent.  I don't know if other large universities do too.  To get comfortable with an online format, take or audit an online class you are interested in.  Also see Dave Kaye's comment, which is helpful.  However, I think that if you can get a credential that would be a plus.  Also, the more experience you have with online group interactions (preferably live) the better you will function when you start doing that kind of work.  The multitasking aspect can be tricky but like anything else it gets easier with practice.

You should get comfortable with several different platforms, including such things as WebEx, GoToMeeting, those sorts of things.  The more you use these platforms, the easier it will be for you to quickly get comfortable using a new platform later.  Your eye and mouse will be able to scan the screen quickly and nail the feature you are looking for.

Coursera has a handful of courses that cover the topic of distance/eLearning that you might find useful. For example Foundations of Virtual Instruction and possibly e-Learning Ecologies: Innovative Approaches to Teaching and Learning for the Digital Age.

There is very little regulation with regards to online teachers, so you probably wouldn't need to get a certification.
False! Not all online classes are on BlackBoard or Moodle. There's Khan Academy, Lynda, and a bunch of other spots online that are similar. Your skype teaching experience is also not irrelevant at all. A lot of these courses do "workshop" style classes, which are essentially group skyping.

A few things about teaching online:

don't expect to be paid a whole lot
if you're looking for something lucrative, it can be way easier to join some sort of tutoring program than to teach traditional classes in an online setting with multiple students
most online teaching is now happening in a pre-recorded video format. Production values seem to keep getting better and better. Have you checked out MinutePhysics?
there are so many ways to teach online. If you're looking for a more standard university experience, plenty of universities have online programs. Occasionally these programs get outsourced, so I would look into the companies that they outsource to. The ones that don't outsource, of course, tend to hire in-house, but I feel like they would be open to a new application. Perhaps that's something to consider?

Anyway, I know this is maybe a less clear answer, but hopefully it will give you some ideas with regards to what your options may be.

Thank you! I agree with you that even life-class instructors are not get paid well, much less online perhaps. But anyway, what I am looking for is a rewarding activities when my mobility get limited. Thanks again and again for your time.

I started working at a local university and when I was promoted to the full time faculty it was expected that I begin teaching two of my classes online.  Very little training and it was off to the races!  We had a lot of teachers who only taught in the online environment and never came to campus for any reason.
So probably the best thing you can do is start developing a relationship with a university that offers this kind of teaching in the first place.  Being pleasant and capable is probably the best qualification you could have.  Never mind the certificate stuff.


text:
How to deal with sources whose authors I don't have good relationship with?
I used to have a good relationship with an author, but now it's broken. However, my work is heavily based on the work of that author, and I'm not sure if citing it without informing them is OK here. Would there be any potential trouble from this? What if they explicitly tell me to not cite theirs? I just don't want to make the relationship worse, because they may not want to have any affiliation with me. But this is just my thought, I really don't know what they really think.

Maybe you could expand on your last sentence? Why should they wabt to tell you so?

I don't really understand why you would inform them that you will be citing them in the first place, regardless of your relationship. Is this a common thing to do in your field of research?

I cannot help putting it as a question rather than an answer: Newton is dead. I want to cite him. Do I need his permission? Or a more mischievous scenario - Leibniz wants to cite Newton on differential calculus. Is he allowed to? Finally, Dawkins - can he stop creationists from citing him?

@FredS no, there is no need. I just don't want to make the relationship worse

If you work is heavily based on their work, you have two choices: 1. to publish your work, citing their work; 2. not to publish your work (if for whatever personal reason they ask you not to cite them, and for whatever personal reason you decide to comply - I stress personal here, because that's the only kind of reason both of you may have).

@Headcrab that would be a good answer. Consider to make it as an aswer

@Ooker I only meant to make a short remark, but OK.

I have no idea why citing their work will make them unhappy, unless you're, like, writing a rebuttal paper.

@xuq01 And you could hardly write a rebuttal paper without citing the thing you're rebutting, anyway.

@xuq01 And they shouldn't be unhappy about a rebuttal. It is different if you misrepresent their work (especially if you make it sound absurd). But just rejecting it? That's how it works. (I admit this may vary by discipline, so maybe rebuttal is more reason to be unhappy in some fields.)

@cfr I guess it depends on the field, and on what is rebutted. In some subjects like where you can't really be totally objective, "misrepresenting" and "merely rebutting" could be difficult to discern. One of my professors during my undergraduate got mad at an negative book review in a journal and had some not-so-friendly exchanges with the reviewer (all in an academic journal). Clearly, to him, his book is being misrepresented, but the reviewer thought they were just rebutting.

Yes, cite the other author's papers regarding any data or ideas on which your own work is based. It is crucial to do so; you MUST acknowledge the other author's contributions to your field if your own work builds upon those. As mentioned by others, unless you are writing a rebuttal, keep a neutral, dispassionate tone in your writing and refer to the other author's papers in neutral terms. Be specific in your citations. And yes, try to avoid having your paper reviewed by this author, at least for now.
The bigger problem was somewhat glossed over. Can you reach out and attempt to repair your relationship with the author with whom you've had the falling out? Ultimately that will be the best for your career, and maybe for your health. You can say, "I perceive we've had this 'time out' but I'd like to apologize if I've caused some problem. Can we meet for coffee and see if we can find some common ground?". Or something like that. It takes courage to go back to someone who has become hostile, but it could be that your load will be much lightened by such an effort. There's the possibility that some misunderstanding can be resolved. And even if you are rejected, you have at least tried. Life is short. I'm hoping for you!

Thank you so much for the last paragraph. I really feel relief to say this: I actually have attempted to fix it many times, but all are rejected, and am perceived as stalker. I just want to avoid all unnecessary negative emotion now.

Agree. Completely.

If you feel that the work is relevant, you must cite it - not citing would be unethical.
Also, most people are happy if they are cited - regardless of their relationship to the person who cites them. Citing someone does not mean liking someone - even when criticizing someone's work, you have to cite.
And if you can think of no particular reason why they should not want to be cited by you, there probably is no such reason.

I can think of one reason- knowing that your work is heavily based on that information and vengefully declining so that you cannot publish it. I'm not saying I would do it, or that there is ever a good reason to do it, but I've met enough stubborn people to know that it could be an issue.

Wow. I could not imagine there are such kinds of people! @jonathanbliss: what do the peole not "allowed" to cite in this situation?

@JonathanBliss, by what mechanism can anyone stop other people from citing their published (in any sense of the word) work?

@paulgarrett I never stated it was possible for someone to do so. But if that's the case then that should be included in this answer, and it is in one of the other answers. So that if (or when) this person is confronted by someone who doesn't want their work cited- they are prepared to address it correctly. Saying that there is nothing to worry about and that they might be happy to be cited no matter what  is a bold assumption about the other person involved.

What would you do if one of these ugly people said "Do not cite me"?

@Udank They do not get a choice in who cites them. It seems odd that you would ever ask anyone if you can cite them.

Yes yes, of course. But giving the fact that there are apparently such odd people, how do the others react than?

@JonathanBliss, I do not claim that people will be happy to be cited no matter what. Only that "published" work is in the public record, and can be referred-to without prior permission of the author(s)! And, in many cases, must be cited, for scholarly and intellectual/scientific accuracy. One has an actual obligation to cite, in many such cases. If I heard anyone telling someone else not to cite, I'd think that they had a serious misunderstanding/problem themselves.

@AustinHenley I suppose private communication might be the exception to that rule.

@paulgarret Jonathan is listing reasons why someone might not want to be cited, not reasons why you shouldn't cite someone or reasons why someone would try not to be cited.

From a more general legal perspective: citation for the sake of the creation of new stand-alone works, especially scientific work building on top of previous work, is one of the rights that the author of the cited work does explicitly not retain exclusively (although they may be entitled to compensation depending on the extent and purpose of citation).

@DavidFoerster Are you sure you are thinking of citing them and not, say, quoting them? I've never heard anybody got compensated for being cited!

I'm not sure not citing relevant work is always unethical. In some cases, an awful lot of stuff is relevant and it is not practical to cite all of it. So you might well cite examples rather than everything.

@cfr: Yes, sorry. I meant quotation. (The legal term for "quotation" in my language has the same root as "citation".)

@paulgarrett Some journals only allow you to cite published sources. Where that's the case, it is tricky if you've read a manuscript online or something like that, since they don't count these as 'published'. (I think this is a problematic policy, but some places have it.) In that case, somebody refusing to publish 'properly' might present you with a problem, I guess.

Yes, you should cite their work. The only reason I can think of for not wanting to cite it is if the other person believes that you have misinterpreted their work and have told you not to cite it.
Even then, if your work is based on theirs you need to cite them. I would be wary, of course of making disparaging comments about their work in a future publication. If you think you have done an improvement over what they have done, let your own work speak for itself. Of course, you shouldn't misrepresent what they have said, but that is true whether you have any personal relationship or not.

I would add that if they do think you're misinterpreting them and you can't resolve this, it would certainly be courteous to explain this in a footnote. Or if you've refined your interpretation, but don't know whether they'd now accept it, you can say that in a footnote. This is not uncommon in my discipline, though perhaps it would be inappropriate in others.

One other thing to add - if OP's work cites this author heavily, it's quite possible that an editor would pick that author to review it. When submitting for publication, OP may want to check for options to avoid this, if they don't feel that they would get a fair review.

@Geoffrey Brent I think you just brought up the only objective reason why citing the other author could be a problem. I'd +2 if i could.

Who you cite is your business and nobody else's. You don't need to ask permission to cite(unless you're reproducing images or something*), and nobody can deny you the right to cite them, for whatever reason.
More importantly, if your work draws from someone's work, you must cite them, it's imperative. No personal equations can change that.
*In this case too, as pointed out by corey979, the permission is for copyright rather than citation, and the parties involved could include the publisher.

If you work is heavily based on their work, you have two choices:

To publish your work, citing their work. If you publish your work without citing your main source, at best you will be asked by reviewers to add a reference to that. Worse outcomes may include your work being rejected as incompetent, you as an author getting on some sort of "black list" as dishonest, at worst, you may get accused of plagiarism and get banned from publishing. Seriously, is there a way for you to mention it somehow, like "well, I was going to cite that, but they asked me not to", so that it isn't perceived as you either unintentionally missing or intentionally hiding the relation of your work to their work?
Not to publish your work, to avoid the consequences mentioned in p. 1. I can't imagine any possible legal or ethical reason for you to do so, but you may have your own personal reasons (like, not to alienate those people even more, etc). For all I know, citing a published scientific paper cannot be forbidden, so you're going to be doing them a personal favor, of a sort, at your own expense. Well, all kinds of inter-personal politics happen in scientific circles, and under some circumstances it may be worth it to have one less mortal enemy in exchange for one less published paper, but that's for you to decide.

tl;dr: Just cite their work.

I'm not sure if citing it without informing them is OK here.

It's ok; in fact, it's your obligation to cite their work, since your is based on theirs.

Would there be any potential trouble from this?

No, absolutely not. If you fail to cite them - then you'll have trouble.

What if they explicitly tell me to not cite theirs?

They can't.
They won't. Really. It won't even cross their mind.

I just don't want to make the relationship worse, because they may not want to have any affiliation with me.

Citation is not perceived as affiliation. Just make sure you don't discuss their work in a way which exacerbates the animosity between you; refer to it positively, i.e. instead of saying "X is deficient, but we can fix it with Y", say "We improve on X by doing Y").

I upvoted everyone else's answer.
I am not adding anything different, but want to tie it together concisely.

Scholarly papers that draw on, reference, refine, or continue some prior scholarly work must cite specifically that prior work no matter who wrote it.  That is your obligation and it has nothing to do with the source's preference.  Indeed the source might be your own previous work.  You cite it, you say what relevant concept or fact you draw from that work, you state clearly and dispassionately what its value is (from the perspective of your work) and you defend that evaluation, especially if it's negative or you say the prior work is incomplete.  Be prepared to defend that in your scholarly paper.  Good or bad or neither.
Sometimes it is hard to decide whether to cite something or not. You do not want to slight another scholar by failing to cite relevant prior work, but you also should not meaninglessly cite work to support another author's vanity.  (That can also include your own prior work.)  You must also be prepared to say exactly what it is in the prior work that is salient from the perspective of your work and not inflate the number of citations just to make your work appear more scholarly or well-researched.
Depending on the salience and relevance of the prior work, you may want to mention the surname of the author (or two authors or primary author followed by "et.al" if more than two) along with the reference number that is usually in square brackets.  Such as:

Shannon and Hartley [4] derive the rate of information capacity of a channel in terms of its bandwidth and signal-to-noise ratio as ...

But if it's a more minor or fleeting reference, it could be just:

In [4] the channel capacity is given as ...

If some scholar has done incomplete work on a subject you are writing, tell us.  If some scholar has done crappy work on the subject, tell us.  If some scholar has done unoriginal work on the subject, tell us (and make a reference to the original work, it's embarrassing but when someone reinvents a wheel, we need the full history spelled out).  No scholar has any right nor expectation to block a negative citation, but the critic must be able to defend the negative expectation.  Do this dispassionately.  Don't say anything personally negative like "How could an expert make such a silly error?"  Just say what it is and how it is in error.
Likewise, if there some prior work that is praiseworthy that is relevant to your paper, cite it.  Spell out the significance and worthiness of the specific fact or concept cited.  And do that dispassionately.

Personally, I think there is a glut of PhDs out there writing a shitload of crappy papers.  Even in my own field (the IEEE transactions are sometimes just full of over-mathematicalized useless crap that is being published solely to boost someone's publication record) I think that.  Those papers should go unnoticed and uncited unless there is a glaring error.
But there are also the few gems out there and if your paper draws on any, you must cite them.

Please, never write something like "In [4] the channel...". References are not nouns. If all references are removed, a paper should still make sense. Instead write "The channel capacity is given as ... [4]."

i'll concede that it's terse and ugly.


text:
Should I write a rigorous draft before asking for comments?
I have a 10-page manuscript of my independent research and would like to ask a professor for comments.  In short, I claim that I've seen a bridge between Shannon's information and semantic information.
The field has been stuck for a long time and I think it might give a breakthrough on it. However, I do see that it isn't really rigorous, and even have contradiction. I know ideally I should spend more time to research but since I need secure funding and getting some comments might be more efficient now, should I ask them anyway? I have also thought about go crowdsourcing, but if I get accepted maybe I won't need to do that?
I've asked some person who knows me, but they are all busy or out of the field.
PS: it is rigorous and not contradict anymore now. Here is the manuscript, I hope that you can have a comment on it. Many thanks. Clearness and Fadedness as a link between semantic information and physical oscillator

Related:
• How can I get a PhD position to work on solving a particular mathematics problem that I have formulated independently?
• Handling unsolicited proofs of famous mathematical problems
• I believe I have solved a famous open problem. How do I convince people in the field that I am not a crank?

If your work contains a contradiction, don't you know it is incorrect?

It can be. But since this is still in the definition phase, I think it can be resolved. Maybe the contradiction is the result of not rigorousness?

It's funny that after asking this question, I see where is the problem

I am skeptical of your use of the word "the" in "the bridge between ... ". You seem to be interested in connections between a technical concept (Shannon's def information) and a much more nebulous concept (how "information" is used in natural languages). There are doubtless various links between the two. To say that something is the link strikes me as implausible. For one thing -- the only way you can prove anything is via a formal definition of semantic meaning, and once you do that you have a brand new bridge problem: what links your formal definition with the natural language "meaning"?

@JohnColeman yes, my English is not so well-defined or rigorous; I'll make it less contradiction. I'm not quite sure about your last point. Do you mean that I can't find a definition that can't really grab the nebulous concept? If so, it's exactly what I propose: to grab a nebulous concept, don't try to make the unseen clearer, but try to make the clearnesses close together. I'd love to send you the manuscript if you want

@user37208 yes, not the mathematical rigor. What I'm proposing is the opposite: to see the meaning inside, you must make it less rigorous. I'll send you the manuscript if you like

It's the nature of the work of academia to throw out interesting ideas and have them torn to pieces, and then to pick out what remains and build it into something publishable.
Since you're in the definition phase and have a 10-pager, I'll assume that you've put together a reasonable literature review and/or theoretical underpinning. What remains is to express the intuitive leap sufficiently plausibly that your oversight (supervisors, funding bodies, university review panel, etc) is prepared to back you.
There's no need to have it all worked out - that's the work to be done. You just have to demonstrate that you might be on the right track. Naturally, the closer that 'might be' is to 'are', the better. But if you can demonstrate this much, feel free to ask for comments.

How do you define "reasonable literature review"? I do read introductory books, and see that's it has been stuck for a long time, but haven't read recent papers. But from the link I can see that it is still going circular.

@Ooker You need to show that you are familiar with what's out there. It's impossible to keep absolutely on top of everything that's just been published (there'll be more by the time you think you're done), but go through some recent journals and attend a conference or two in your area. You can ask more experienced researchers in your area for advice on how recent the papers you review need to be. A couple of journal acceptance cycles (how long it takes from submission to publishing) is probably reasonable.

@Ooker To merely ask for comments, you're probably fine with being conversant with the established theories. I'd still suggest going to one or two relevant conferences to get a feel for current research, but it's going to be the intuitive leap that you need to express. The lit review helps establish that you're not a 'crank' but it doesn't justify you asking for their time - it's your original ideas that justify that.

it's also not really fluently in English. Is this a problem?

@Ooker It’s not a problem unless the person you’re asking deems it a problem. You’re just asking for an opinion on your potential research, right?

yes. It's just that I'm worry to be seen as a crank.

typically how much time does it need to have a reply? I've sent the 20-page, rigorous and non-contradiction manuscript two days ago to some professors and haven't received a reply yet. Is that worrisome?

@Ooker That's a separate question, but 2 days isn't a lot of time to go through a 20 page document, especially if the reviewer is busy with other things. You might want to ask them to give you some idea of when they think they might be able to reply.


text:
What does "Your submission will be handled by Receiving Editor" mean?
I submitted a paper to a journal and after 20 days I got an email which states

Your submission entitled "X" will be handled by Receiving Editor.

What does this mean?

It looks like a confirmation that the paper will be handled by a certain editor. I would say it is basically a confirmation of submission.

Another possibly related question: https://academia.stackexchange.com/q/55665/45543

@Christian thank you, i am still confused to know what it means. Do you think it is an indication that the journal wants to invite reviewers?

To me it looks like they assigned an editor who will then decide whether to send it to reviewers. It might be that the paper passed some managing editor but I think it is impossible to tell from this message alone.

Here's one journal spelling out the receiving editor's role at their journal. The journal you submitted to might or might not use the title in a similar fashion.

@Anyon thank you, i guess it is just an editor assignment for my paper. In your mentioned link it means that the paper will be sent out for review and i don't know if it applies to my journal or not.


text:
PhD admission possible without research experience, but 30 years of corporate experience
My question is about PhD admission.
Is it possible to get admission to a PhD program in organization culture in management without any research experience? I have 30 years of corporate experience.

Which country/countries are you interested in? Do you have a bachelor or master's degree?

Yes, particularly if you pay $$$.

depends upon your qualifications and the program's requirements. Hence the answer is specific to you

Just to comment... the purported goal seems unlikely to serve any substantive purpose. Could you clarify what your further (ultimate?) goal is?

The short answer is "yes". The long answer is that departments look for (i) candidates for which the department's resources for advising students are likely well spent, (ii) candidates likely to graduate, (iii) candidates likely to be productive contributors to the research mission of a department, (iv) candidates who after graduation are likely to further the reputation of the department in some way or other. For public universities, there is also (v) the requirement to support the public good in return for the tax money provided by the state, generally by providing an education to those who will then go out and join the work force.
As a consequence, there are arguments for and against admitting those who join after long stints in industry. On the plus side, these are people who know why they want to go back to a university to get another degree, and they're often motivated to get through the program quick and successfully -- they aren't there because they haven't figured out what to do with their lives and for whom going to grad school was the path of least resistance.
On the downside, people who have been in industry for 30 years are in their 50s, and it's not quite so clear as for a 20-year old (i) what the benefit to society is in providing them with another 5 years of education, given that they're likely going to retire soon, and (ii) they may have a lot of industry experience, but may not be up to date on the prerequisites for the graduate program.
So yes, programs often do accept people into a graduate program who have been in industry for a long time, but the considerations are complex and varied. Make your case in your personal statement for why the department should accept you!


text:
If I decline to join a Master's program, can the university deny admission to me if I apply on the next year?
Suppose I get selected for an American/Canadian University for a masters in computer science as an international student for fall 2022 , but I decline to join the university due to some personal reasons. Will the university save my application details?
Could they deny me admission if I re-apply to the same university in the next year?
Furthermore, does any university provide a provision where I can defer the admission to the next year?

You are better off accepting to join, and immediately asking to pause your studies.
Get in touch with the enrollment office: you can be transparent with them, plus each university may have different rules

Deferring admission is not uncommon (and often used during Covid). Whether they will or not is up to them. Unlikely the university wants to save applications - that is a headache of personal information to protect. If you reapply, it is a new applicant pool and there is no way to know how you would stack up against the new pool.

Is it possible for a university to reject my application on the next year just because i had declined to join in the previous year?

Yes
Declining is not the same as deferring. If you defer, then you are effectively still admitted, you just do not attend that year. If you decline, then you are saying you will not attend. The university will call up students on their wait list, and forget about you. If you change your mind you'll have to submit a new application next year, and deal with the changing circumstances - e.g. your (new) competitors, the funding situation, COVID, etc. There is no guarantee you'll be accepted in the new round, although it's not impossible either.
As for

Furthermore, does any university provide a provision where I can defer the admission to the next year?

You'd have to ask the university. There's a good chance the answer is yes, but you still need to ask.

The comments give good advice (EarlGrey and Jon Custer), but to answer the question, I think it would be unusual to turn you down for that reason alone. If you have already told them no, then you can try again in a year. But, in a competitive program the outcome might not be the same next time, so if you haven't yet acted, try to accept with a deferral.
In an interview, you might be asked for reasons. Be prepared with an honest, but convincing reason.


text:
Can MOOCs help me improve my profile for an MS in Computer Science?
I wish to apply for an MS in CS in the United States or Canada for Fall 2022. I am from non-CS background (engineering physics) and currently work as a software developer.
I had programming experience in college and took undergrad courses in data structures, algorithms and machine learning. But I have not taken core CS courses like operating systems, compilers or computer architecture.
If I take any online courses on these topics and mention the certificate link in my statement Of purpose, can it help boost my profile?
Considering the fact that I would need to start applications 6 months from now, I was wondering if such online courses are worth the time now.
If yes, can someone suggest online courses on these topics which have the same level of rigor as an undergraduate course?

The best way to show your course material is to present a project along with it. A good part of your application will depend on projects. If you can manage something "your resume" worthy, it should hold way better than simply mentioning it on your CV.

The problem with such online courses is that it is very difficult for an admissions committee to verify that you actually learned anything. If you work hard at such a course and do at least as much as the course requires then you might learn something useful, but it is very difficult to equate such a "credential" to a proper university course.
So, such things won't hurt and you might get a chance to answer questions asked if you get an interview, but don't depend too much on them.
On the other hand, US admissions is based on a broad assessment of the likelihood of success in the program so it might be that some online courses could help fill in the broader picture.
But the knowledge is more valuable for the knowledge rather than any "credential" or "boost for admission".

Since you mention Statement of Purpose, let me give my standard advice. Don't spend many words there talking about the past - what you have done. Use those words to focus on what you will do in future - plans and goals. A short phrase noting how past things support those goals can be fine, but it is the CV that focuses on the past. So don't miss the opportunity that the SoP is intended to provide.


text:
Why is my published article seemingly not indexed by Google or Google Scholar?
I am a Masters student, in the Faculty of Science in Canada. I have a question to ask regarding literature review. I am doing a bit of studying to find protocols for my experiment (where I hope to conjugate a certain linker to a nucleic acid). I tried looking for papers with different keyword searches on Google Scholar, as well as the WebOfScience.
There could be different possibilities here - either there are no papers that have been published, or the Search Spider was not able to find the papers (which is a False Result).
I therefore tried looking for a paper which we had published 4-5 years back in Journal of Chemical and Pharmaceutical Research. It does not show up in the search results, probably because it does not have enough citations (you can try by searching this paper on Google standard search, and on Google Scholar: Potential inhibitors against acetylcholinesterase and glutathione S-transferase associated with Alzheimer's disease).
Doesn't this give false hope to certain researchers, that the work they are currently doing is novel; or make it difficult for other researchers who are trying to find a protocol to adopt?
Hoping to get some insight from the community.

I would be surprised if citations had anything to do with Google's indexing system.

Not Sure. But, it looks like a lot of papers do not show up on Google's or the WebOfKnowledge Databases.
Therefore, my scepticism lies in how much of papers/works that have not been accounted for. Does it mean that one would need to go through all possible databases to come to a conclusion whether a work has been previously done or not? This seems like an awful lot of work to do even in the age of computers. And there is always a possibility that one might miss out on certain sites.

I've just googled the title and the first result I get is your paper's page on ResearchGate.

I won't put this as an answer as it may not be right.  Your paper appears in the journal "Journal of Chemical and Pharmaceutical Research" by the publisher Omics.  Both the publisher and the Journal are considered to 'predatory journals' (e.g. https://bradleymonk.com/Beall%27s_List_of_Questionable_Journals).  I believe that Google Scholar, WoS, Scopus, etc do not list these types of journals.

Then, is there a possibility of a conflict in copyright when some assume their work is novel based on the journals that are available on the well-known search spiders? I saw the link @HoboSci mentioned, it has a lot of journals which is not humanly possible to go through individually. Just curious.

@semdeb - well to some extent, all work is science isn't novel as it's built on the work of others. In my field (marine biology) there are many papers that use tools that have been used before to answer questions that have been asked elsewhere.  What makes each study novel is that they may run things a little differently, or apply a tool/method to a new species/location/situation, cross between theoretical and empirical work, etc.
The only conflict that may arise if you 1) cite a paper from a predatory journal (it may not be allowed) or 2) you copy from a paper in the hope no-one spots it

@Somdeb, when you ask about novelty and copyright, then that is a completely different question, worthy of a new post on Academia SE. If you post a new question on that and tag me (maybe by mentioning me in a comment), I'll be happy to offer a response; you'll probably get lots of good responses from others as well.

If you setup a Google Scholar profile, then I think you can manually add citations. I don't know whether this leads to inclusion within Google search.

Can someone mark this question as SOLVED? I am not able to edit the title.

Although you asked a generic question, the answer is very particular to your own particular article. Most likely, @HoboSci, got the correct answer: you published in a journal of questionable ethical editorial policy that Google Scholar refuses to index. That is, "Journal of Chemical and Pharmaceutical Research" is probably such a journal (see https://bradleymonk.com/Beall%27s_List_of_Questionable_Journals).
I looked up the issue where your own article is published: JOCPR Volume 6 Issue 3: http://www.jocpr.com/archive/jocpr-volume-6-issue-3-year-2014.html. I searched Google Scholar for your article "Potential inhibitors against acetylcholinesterase and glutathione S-transferase associated with alzheimer's disease". I also searched for a couple other articles in that same special issue and none of them showed up in Google Scholar.
Unfortunately, I don't think there's anything you can do about it because once you've published in a journal like that, you can't republish the same article anywhere else. So,the lesson is to only publish your work in reputable journals, or else your published work might become almost invisible on the Web. :-(

Could OP republish the abstract on his own webpage, with plenty of helpful keywords?  Do you think that might help?

I doubt that would help. The full article is already on ResearchGate, which is well indexed by Google Scholar, yet Google Scholar still doesn't list the article. So, I doubt posting something on their personal page would help. I suspect that once Google Scholar detects the journal name, it refuses to index the article. Perhaps one way to get it on Google Scholar would be to remove the journal citation information from ResearchGate.

It looks like; the question has been changed. But, my question was not concerning my published paper. It was only an example. As I had explained in the description that I am doing some literature review for my project, however, I am unable to find protocols for some of the steps. Hence, I was just wondering whether there aren't any protocols or if the indexing service doesn't pull up papers. I guess @Tripartio mentioned it in his answer, that the papers could be in unreputable journals. But, even if they were in unreputable journals I could at least have an idea about the procedure for my expt

@Somdeb, the point is that there is no generic answer that fits all situations. There are many reasons why any particular article might not be indexed that you otherwise might suppose to be. You have to specify the exact article and then investigate the exact reason. So, for the example you gave, we gave the specific reason to the best of our ability. If on the other hand, your question is, "How can I trust that if I don't find something on Google Scholar, how can I be sure that it doesn't exist?", then that is a completely different question. (Short answer: you can't)

@Tripartio Thanks for the answer now it is a lot clear. Sorry, I did not get back earlier.

This probably has nothing to do with predatory publishers or with the number of citations. Google Scholar has no quality requirements - it indexes anything and everything. This is unlike Web of Knowledge, which does have quality requirements, and also why Jeffrey Beall has said Google Scholar is full of junk science. What's likely is that the publisher didn't provide Google Scholar with what it needs.
Although Google Scholar has no quality requirements, it does have certain technical requirements before its bots can even crawl the journal's website. A key requirement is that Google users must see at least the complete abstract or the first full page. There are other technical requirements, as can be seen on this page.
Since it's not hard to get indexed by Google Scholar, it is something that authors should demand from publishers, and if the publisher does not do this, authors should approach another publisher. However since you can't retract the article, the next best thing to do is to host it on your institutional website (see the "Individual Authors" section in the last link for more details). If you don't have a website, you can also hand the article to your university repository. There's probably nothing you can do to get indexed by Web of Science however, other than hope the journal someday gets indexed by SCI.


text:
Citing unpublished figure from an ex colleague
A former colleague has created a figure. The figure is not published and serves only as a mean for information sharing. I used to be a part of that research group and thus had access to it.
I published an article featuring a modified version of this figure, to explain my current experimental set-up. I did not cite the author of the figure as the figure was not found in any published material. I didn't know what to do - perhaps add them in Acknowledgments?
Have I done the wrong thing?

No. It's just a very high-level description of an experimental set-up that the entire group uses.

They do care. They are accusing me of plagiarism.

The correct thing to do is to cite them for the figure by name, if they will permit it. List the citation as "private communication". You should also probably indicate the it is "adapted from a private communication..."
You have committed plagiarism if you give the impression that you are the source. But it is easy to avoid with a citation.
You can probably handle it in acknowledgements if you are clear about what you are acknowledging. Use language similar to the above.

Okay. Thanks. I didn't know about this and it was revealed to me several months after publishing the paper. Do I need to contact the publisher now? What do you advise?

It is hard to backtrack and I don't have advice. You could try that. But you could also, at least, apologize to your colleague. I doubt that it would be noticed by anyone unless your colleague objects to what you did. But use better practices in future.

They did object, accusing me of plagiarising the figure. I will happily apologise as I wasn't aware of what better to do in this situation. But I would of course like to amend the situation, too.

Since they objected, it would be best to contact the editor to see what sort of clean-up can be done.

OK. I've done that. Let's see what happens. Thank you.

Citing such "private communications" is often frowned upon, because others can only take your word for it, and have no chance to check the context.
Like with any illustration that you copied or very closely adapted from somewhere else, you put a copyright notice (after asking for the consent of the copyright holder, that is) in a footnote.
The facts represented in such a figure deserve an additional citation, if they were previously published. If not, no problem, but you are automatically taking over the scientific responsibility for their correctness.

But it was already published. So, contact the editor to add a copyright notice?

You cannot modify an already published work. Not to correct a misspelt name, not to add a citation,  not just add a copyright notice.