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Can I work full-time (remotely) while doing a PhD in Science?
I will hopefully be starting a PhD soon, it will be in the sciences (so at least several hours a day will be spend in labs). It is a 3 year position, with a possible extension to 3.5 years, and it's in Europe.
It is possible that I will also start a job around the same time. It would be a remote job, in the same time zone as my PhD. It wouldn't be for the whole duration of the PhD, as the work position is limited to 6 months.
I know that a job and a PhD at the same time will definitely be difficult, but I really want to do both, and think it should be okay with good time management (e.g. my lab work will involve centrifuges a lot, so I could get some work done while the centrifuges run). Just want to get a second opinion to see if I'm being too optimistic about this?

this answer of mine on a different question might be also relevant .

Getting a job position for 6 months is not beneficial for your CV, you will not learn much, you will also not be so productive. The question is then: why? financial matters?

@Anton Menshov Thanks for those! I had already seen them but was hoping that the job being remote would maybe change my chances of managing both, which as I can see now is not the case...

@Roland Yup no problem from the funding side of things

@EarlGrey yes unfortunately some personal financial matters, so I could really do with some extra income. I asked if there were any graduate teaching positions but unfortunately not a thing at my uni. Also, the company is one of the biggest names in my field, so I thought it might be good to build connections there even if I don't actually work for long. During my undergrad I thought I'd change fields and my summers were spent on internships in another sector, so I don't actually have any work experience in my current field yet.

If you plan to work in a company in the same field as your PhD, without having a research agreement or a research project, it can actually be a big source of issues/problems/breach of confidentiality and so on. Don't do that. You will have your PhD epxerience speaking for yourself in 3 years, you need no connections right now. If you are ready to work some extra hours, try to be tutoring highshool students, or university students. You don't speak the local language? don't worry ... rich people sends their offsprings to international school where the subjects are all in english!

Would you stay in the lab observing the centrifuges, while you work a remote job for some company?

@BernhardDöbler very good (and obvious, I missed it!) point ... put it even clearer and in indirect form: "If ou are the lab head, would you be happy your employee is doing another job while you expect him/her to work on the centrifuges (i.e. work and control, even if everything is running fine)?"

I'll focus on the formal/legal aspect of your question, as the issue of practical feasibility has been covered in other answers (in this and the linked-to threads). A second full time employment will most likely be impossible for formal/legal reasons alone.
In many places in europe a "PhD position" means you are an employee of the university. Sometimes these are part-time and sometimes full-time positions. If full-time, you have a contractual commitment to work 36-40 hours per week for your university, so this would absolutely preclude another job. If part-time, the contract would most likely require you to seek assent from your superiors, e.g. HR but de facto your supervisor, for any other employment you take on. The expectation with part-time "PhD positions" is that you work on your PhD project in your spare time and on your employment duties (teaching, research, administration) during your work hours, even if this distinction is often fictitious. You won't be able to do this if your spare time is consumed by another job. Thus you probably will neither receive assent for taking on a second position with any significant work hours nor have sufficient time for your PhD project anyway.
There is one exception, namely that the second job directly contributes to your PhD project. For example, industry internships in an applied/engineering filed, or government internships that allow you to conduct participant observation in political science are not uncommon. Nothing in your question suggests that this exception applies.
Moreover, the contract for your prospective second job will most likely also preclude you from taking on another full-time position.
You will have to talk to your supervisor about this, but it sounds very unlikely that you will be permitted and/or able to work full-time while being on a PhD position. If you are dead set on the second job, you could try to negotiate a later starting date of your PhD position and consider already enrolling as (self-funded) PhD student before. But even then, your chances of success are small, because your supervisor probably wants to fill the position soon.

I disagree that 40 hours per week contracts exists for PhD students. Please provide a concrete counterexample.

@quantum just Google it. Here is one recent example: https://population-europe.eu/study-career/full-time-phd-position

@quantum Many PhD-students in Germany in MINT work under the public service contract framework TV-L in full-time.
What's full-time varies for each state (Bundesland):
https://oeffentlicher-dienst.info/tv-l/allg/arbeitszeit.html

Yeah your assumption is right, my second job wouldn't contribute to my research. My PhD contract doesn't specifically disallow me to take on another full-time job, but I didn't think that my job contract could potentially do this (I haven't really worked before, part of the reason I wanted to do this), thanks for pointing that out!

@IsabelleRoth Note that the contract may not need to disallow this for it to be disallowed. For instance, the work contracts at German universities often only have 1-2 pages, but the 112 page public service contract framework is also binding. And even that doesn't disallow a second job, and only contains the clause that a second job needs to be authorized. And this authorization will not be granted if taking up the second job will make you violate the law stating the maximally allowed numbers of hours worked per week.

If you are in France and get a public funding, you need an explicit authorization of your lab and institute to be allowed to do something in parallel, and it is only allowed 1) on your free time or 2) during, but for very specific missions (teaching, outreach, expertise related to your PhD).

Yes, you are being too optimistic. As soon as anything goes wrong (i.e. your second job has some issues, or the centrifuges do not run as smooth as predicted) you will end up under huge stress.
And a PhD is already a lot of stress, especially in the first ... 4 years.

The link to other answers will tell you the same thing as I summarise in a few words: PhD is a full-time job. The relevant question you should ask is: can you do two full-time jobs?
Also, many works contracts in Europe prohibit a second job in written.


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How do I ask for an advanced topic to a Prof?
I asked a prof for a project and he gave me a book to read. However, I am already familiar with its content(I did an online course). I want to request him to change my topic.
Is it okay to ask for a change? How should I do it?

more details please. Is this a thesis?

@quantum It is a undergraduate project

The title mentions an advanced topic, the body of your question only a different topic. Which is it?

Taking an online course and thoroughly working through a book are two different things.

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How many publications is seen as a good number for a Ph.D. thesis defender in CS field?
I know that the question may sound a bit context related (country, university, topic of the Ph.D.) but in general nowadays, how many publications (conference + journal) are Ph.D. students required to have to safely present at their Ph.D. thesis defence ?
Thanks.

It could be as low as zero, actually. But it depends on place and the form of the thesis. Where are you asking about?

norway and germany

As you suspect, it depends on context. Most of all, it depends on the subfield. In machine learning, for example, the rate of publication is much greater than in other fields, e.g. multiple papers per year; where in some areas, such as theory and systems, it can be that one spends 3 years working on a single major paper or result.
Also: most fundamentally, graduation is not dependent on meeting a certain publication threshold; rather, it is up to whether your advisor wants you to graduate and whether you have met all the requirements of your program.
With these caveats out of the way, a general rule of thumb is at least 3 publications for which the student has made a primary contribution to, and which are in the same or a similar topic or problem space.
Notes on this:

"Primary contribution" usually means first author or shared-first author; the question is whether that paper can be included in the student's thesis. If the student is not first author, then  they should at least be closely involved enough that they can take responsibility for the paper content.

"Similar topic or problem space" is quite subject to interpretation. It may be, for example, that two unrelated papers can be compiled together in the same thesis if the author can find a way to tell a story of how they are related. I have even seen theses that simply have two parts, and the introduction will say "Part 1 is about problem A, part 2 is about problem B."

It is common for PhD students who publish less than their peers to graduate anyway, if they and their advisor want them to. For example, if a PhD student reaches their 5th or 6th year and they only have 1-2 papers, but they have already found a job, they will likely be able to graduate with their advisor's endorsement.

Finally, you should look to a particular institution and/or a particular advisor for specific requirements, either formal or informal. It is likely that more competitive universities will have a higher publication standard compared to lower-tier universities. And some advisors consider the exact publication count to be important, while others do not.

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Do you have to be married for spousal hire?
My partner and I are both in academia - he is a medical fellow and I am a PhD candidate in biology. It looks like I'm going to be defending in about a year or two and he will likely be finishing his fellowship in 2 years. This means that we're going to be in a position where we're looking for long-term positions at the same time. We are not married nor engaged, so I fear that  a spousal hire may not be offered if we are only partnered. Of course, in this situation I would be the one that is the spousal hire and not him. Also in this situation we are hoping that he gets funding to impress a university.
How have you all fared with spousal hires  specifically in the US and Canada? Or what have you all heard?
Thanks!

Would your partner be looking for a job at a university or a hospital? If a hospital, then that usually would not be the same institution, even if there is a university affiliation for that hospital…

Or are you thinking you would be the spousal hire within the hospital or hospital-affiliated labs?

Would your partner be looking for a job at a university or a hospital? That is a great question. I assume that he would be willing to work at either. He is aiming to to be more of a researcher rather than a physician and alot of his research work so far has been computational. I am open to working at hospital-affiliated labs as a tech but we might be more likely to find a university rather than a hospital that fits as both.

This will depend on the institution's policies. But for most places I've seen, no, you don't have to be married. Most policies will talk about "domestic partnership" instead of marriage. The rules can differ for other issues related to the hire, for example, health insurance.

"How have you all fared with spousal hires specifically in the US and Canada?"
I fared rather dismally: my (now ex-) wife was in medical profession and I was in mathematics. I had to change the location twice: first time when she finally got a long-term job and second when she lost it in one place and found it in another state. Once I was even seduced by my friend to accept an invitation to be a speaker at the ICM: he claimed that "if I agree, the university would certainly assist me with finding a job for her in the area" (that was when she was looking for a new job after she was told that her contract wouldn't be extended), but nothing of the kind really happened though I honestly went there.
I should say that all places I worked at were very accommodating as far as my own needs were concerned and allowed me long absences and such when we were living in different states with a small daughter (the longest commute was from Michigan to Vermont: an 11 hour drive through Canada one way) and I'm really grateful for that, but as far as finding a job for a spouse, they either could not do anything or weren't willing to and I'm not guessing which one was the case.
A former postdoc of mine was a bit luckier: they hired his wife to one place and himself to another 4 hours (by car) away. They were able to reunite 2 or 3 years later. But they were both mathematicians, so everything could be decided within a single department, which usually makes negotiations much easier.
As far as I see it, formal marriage is not really required in most places in the US, but being in different fields can subject you to all uncertainties of the political relations between different departments (from my perspective biology and medicine are, of course, closer than mathematics and medicine, but they are still not exactly the same thing). I wish you all the luck, but be ready for a bumpy ride at least in the beginning and try to be flexible and consider sacrificing some of your ambitions if you value your relationship.
Everyone's experience is different of course, but you asked and here are my 2 cents :-)

Obviously it may vary from university to university. But in most cases, if university likes you to join them, they try to make the offer as attractive as they possibly can. I have seen them helping find a job even beyond the university. Usually these terms are not written in stones and have to be negotiated. If a new faculty a university  is  interested in and said they love the job but can’t move as their partner also needs to find a job. The things they typically do is try all avenues to accommodate the request but nothing is guaranteed (spouse or not)

You should make the right decision. You will be defending your thesis in 1 or 2 years, that means you have enough time to know your partner more. You are interested in spousal hire, which means you want to be with your partner in the same institution, which means you are likely committed in your relationship, so it is better to take final decision about your relationship when you start at job at same institution. After knowing each other enough, if you are determined about the relationship, then marriage is beneficiary in every way, either in ethicality of professionalism in your future work place or in social perspective. But if you are not sure about your relationship even after 1-2 years, then you should think carefully about joining the same workplace. So at first get out of the complicated zone by deciding something suitable for you.
Regarding your question, it depends on the institution you would want to work with. Certianly there will be less choices if you are not married with your partner compared to the situation when you are married with your partner. People might not flag your relationship status directly but might have hesitation in their mind when hiring you and your partner.

I don't think it's appropriate to give OP advice on whether they should get married.

@BryanKrause, sorry it was not my intention. I just wanted to explain to take the right decision. Either this side or that side, rather than keeping in the complicated zone. Ofcourse this is personal opinion/suggestion.

I'd guess that in the US and Canada, any couple could make it known that they are a "package" and require some accommodation if an offer is to be considered. I wouldn't assume, however, that you are the lesser quantity in that package as your skills might be much more valuable to an institution than (gasp) a medical person.
If there is no possibility of considering the package they will let you know and you can look elsewhere. But you have to make it clear. A university has to be convinced that both (each) of you are capable and potential contributors to the overall mission. No one rides for free.
You might also consider looking in places that have several universities and, perhaps find a pair of jobs at nearby institutions. That doesn't necessarily mean NYC or Stanford. Even in my rural location there is a State university and three four liberal arts colleges within an easy commute. Several community colleges as well. And several hospitals, though they aren't research hospitals AFAIK.

"No one rides for free": True most of the time, unless you are some kind of superstar. Not very likely directly after a PhD, but also not impossible.


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What skills are necessary to become President(Rector, Chancellor)?
Recently on my University he dies and now I was wondering how should be the ideal candidate. Taking into account that he/she is the one above all the faculties.

Does he/she need to have a Doctor degree? and of what kind?
Does he/she needs to speaks more than just one language?

Maybe you could explain a bit what the job of Rector involves at your university. For instance, US readers will have a hard time making sense of your question otherwise, since the title of Rector doesn't exist in most US university systems.

I am certain this is country-dependent.

This will vary hugely between countries and individual universities.
In the UK most universities are formally led by a Chancellor: see this link for more information. Since their role is largely ceremonial, what is important is that they are people seen as being prestigious enough to represent the university. The current Chancellor of Oxford is Lord Patten, who used to be Governor of Hong Kong and chairman of the BBC trust. To the extent that a chancellor may sometimes publicly advocate for the university (especially for funding) it's also valuable for them to be something of an 'establishment' figure on good terms with those in positions of power.
If you mean to ask about the qualities of the person who actually controls the university (which in the UK would normally be the Vice-Chancellor) that deserves a separate answer, but one would expect them to be experts in the education sector and experienced at leading large complex organisations.
To answer your numbered questions:

It wouldn't normally be a requirement that they be a doctor.
I imagine speaking multiple languages would be a benefit (particularly speaking English in a non-English-speaking country), but I can't see it being a formal requirement.

It is probably similar to the skills of a ceo, the position is about leadership, management, teamwork and being able to represent the University. Although an experience in academia might be tangentially useful in order to relate to the people working in the university, their job is so broad, they work with so many people on different levels that this is potentially irrelevant.
You can look at previous people who held the position to work out whether certain universities have more specific requirements.

In the US, many university presidents will have their CV available online.

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How to Offer Review Services
A booknote of mine was just accepted for publication. I've been in contact with the editor throughout the process, and want write an email thanking him, and also indicating that I'd be happy to be considered as a potential reviewer in the future. What would be an appropriate way to phrase this email?

"Dear Editor,
Thank you for accepting my booknote for publication. I'd be happy to be considered as a potential reviewer for your publication in the future.
Best wishes,
user82138"

Perhaps this is facetious, but as far as I know there's no special code that needs to be invoked when communicating with journal editors. Concise, plain English will certainly suffice.

As a journal editor, I agree. The only thing you might add is an indication of areas of interest and specialization, and/or a CV.

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Is there common policy in universities about departments or faculty/staff intervening in the case of misconduct related to Title IX?
My understanding of Title IX is that it is a federal law that requires, among other organizations, universities, to ensure that women are not denied equal opportunities.
In order to ensure compliance with this law, universities create their own policies that they believe tackle relevant misconduct like sexual harassment, stalking, and other related behaviors. However the Title IX office of a university does not attempt to tackle behaviors that fall outside of ensuring compliance with the federal law.
Usually, faculty and staff are required to report or consult with the Title IX office if they become aware of misconduct. I have encountered the belief that once this occurs, faculty/staff are prohibited from engaging on the matter further. I have asked a question on Law Stack Exchange about the legal basis of this belief, but here I want to ask about university policy.
Are there common (or if not, at least notable examples of) policies that prohibit a department, or faculty/staff, from acting on information about misconduct relevant to Title IX further? For example, can a department chair enact sanctions on a perpetrator? Can faculty confront the perpetrator and demand their behavior cease? Can it even be discussed?
Note that again I am not concerned here with the law, but only with university policies.

University policies are going to vary from university to university.  You'd need to read your university's policies and/or talk to someone in your local Title IX office.

What is the policy at your institution? Then it is easier to discuss the differences in other institutions

While specific policies will vary from university to university, there are likely to be general "best practice" tendencies that are shared, which the current answer I think does a good job of discussing.

I have encountered the belief that once this occurs, faculty/staff are prohibited from engaging on the matter further.

I am a former department chair at a large US university. I don’t know what you mean exactly by engaging further, but this belief sounds mostly false to me, or at best a distorted or misunderstood version of something that’s true but doesn’t quite mean what you think it means.
At my university, the department chair will typically remain involved and play an active role in coordinating the university’s response to the incident, usually in consultation with the Title IX officer or similar campus officials. The chair may be advised to not act independently of the title IX office or prior to consulting with them (and even more so to not act without keeping them informed), but it sounds inaccurate to describe this as a “prohibition”. And it’s not the case that the chair hands over the matter to some outside department and then steps away completely from the situation, as the belief you describe seems to be suggesting. (On the other hand, it’s possible that that is in fact the way things work at some US universities.)

For example, can a department chair enact sanctions on a perpetrator?

Department chairs have a fair amount of independence to do things at the departmental level. So generally speaking, I’d say that yes, the chair can do such a thing, but whether it would be a good idea or recommended practice would depend on the specific details of the situation, and in the absence of more information I’d assume it wouldn’t be either of those things.

Can faculty confront the perpetrator and demand their behavior cease?

Yes, similarly to the above: people can do all sorts of things, but if the matter is being handled by the Title IX office, most sensible people would recognize that letting the professionals (with the appropriate training, legal and psychological background etc) handle it is the best course of action.

Can it even be discussed?

Not sure what you mean by this exactly. Information about sexual misconduct accusations would generally be regarded as confidential, but department chairs and certain other administrators would have a legitimate need to know and discuss such things, so yes, obviously they can discuss them. On the other hand, they would need to exercise discretion and not share details with random people who don’t have an official reason to be involved.


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How do editors publish in their own journals?
I was invited to review a paper in which the journal's Editor-in-Chief is a co-author. I do not mind, but raised the question that this peer-review is no longer blind. The co-author can see who wrote the reports.
I do not say the editor takes advantage of his position, but the peer-review is not actually the same.

The details  will depend on the journal, but I know that some have special procedures in place for this case. It is not in itself a necessity that the Editor in Chief knows the identity of each reviewer.

As far as I know sometimes editors can write what they want without reviews but of course it doesnt carry the same prestige and is not considered "scientific" in the same sense as if they wrote some journal where they are not editors but must follow review procedure.

In such cases, the editor-in-chief should recuse himself from having anything to do with the review process. This gives the associate or deputy editor for the given paper essentially full control of the process. (In general, I don't think the editor-in-chief is aware of exactly who is assigned to which manuscript.)
One would hope that the editor-in-chief would know the quality and standards required to publish a paper in her own journal; however, should the paper fail to meet those requirements, you should, of course, call that out in the review.

How would they maintain blind review in such a case?  The editors have the author list.

@Ray: I don't really understand. To whom is the review supposed to be "blind?" (In almost all of the papers I've been asked to review, I know who the authors are ahead of time!)

@aeismail most journals I have heard of review is supposed to be double blind to avoid social, economic or any other unscientific bias.

@mathreadler: As I said, in all of the journals I review for (chemistry, physics, chemical engineering), the reviews are blind to the authors only.

[at]all many a times, as @aeismail suggests, it is actually single-blind review.

Surely, if the journal standard was to make the review process blind for the reviewers, there would be absolutely no problem in implementing this even if the Editor-in-Chief is a coauthor. The only potential problem is in the opposite direction, as under normal circumstances, the E-i-C has access to the information who reviewed which paper in their journal.

@aeismail It must be field-dependent, then.  In computer science, a lot of conferences (but not all) have us submit an anonymized version of the paper in which we remove the author list and potentially reword things like "In our previous work [citation].." to "in [citation], the authors..."

@EmilJeřábek For the reviewers, yes.  But the editors who look at all the reviews and rebuttals and make the final decision do have access to the author list (and need to, so the authors can communicate with them to clarify any issues that arise).  And making the final accept/reject decision when the EIC is a co-author definitely involves a conflict of interest.

@Ray That’s what I am saying, no?

@Ray As I mentioned, the EIC should recuse herself in such a situation.

@aeismail I believe the question is this: How can I, as a reviewer of the EIC's paper, be sure that the EIC won't be able to find out my name on a whim (or accidentally see it while browsing the online system), say, two years from now? Do journals have a system that makes "recuse" something else than "I promise not to look"?

@JiK That and "How can I, as the editor who makes the final decision on the EIC's paper, be sure...".  And "How can I, as the editor who makes the final decision on the EIC's paper make an unbiased decision when I know the EIC wrote it".

I've reviewed a paper by section editors in their own journal.  I can't speak to common practice, but for this particular paper, in this particular journal, the practice was to simply assign the paper to the editor of a different section.  My assumption is that confidentiality was maintained.  I imagine the handling for an editor-in-chief would be similar, and that the paper would go to a section editor who would handle everything.
In this particular instance, I can't say I was real happy with the outcome.  There was a major mistake of interpretation of the manuscript.  The other two reviewers simply missed it (don't get me started about referees who choose to do no work!!), and just about recommended acceptance with no revisions, and my recommendation was much more harsh .   The author acknowledged the error and rewrote the results and discussion-- changing the paper from "Earlier investigators found 'A', but using this new method, we find the exact opposite of 'A'" to "We find 'A', just like everyone else", making it a much less important contribution.  I felt that if the author were not a section editor, the paper would not have been accepted to that high profile of a journal.  I don't think I'd referee under those circumstances again.

"The other two reviewers simply missed it (don't get me started about referees who choose to do no work!!)": Please, avoid accusations you cannot really prove: as much as the authors missed the mistake, also the reviewers could.


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Is it OK to get external help during your PhD if it is acknowledged?
I am starting a PhD, and an interested in getting technical skills I will need over the next few years.
Are there any ethical issues with paying for people to help you to get these skills, assuming they are fully acknowledged?
From what I have read, I am working with the assumption that it is OK, as long as they are not "contributing to the research". However, this seems a bit fuzzy to me. Where does the boundary between the acceptable and unacceptable input lie?

Have you checked this? http://academia.stackexchange.com/questions/38023/would-it-be-ethical-for-a-computer-science-phd-student-to-hire-an-assistant-pro

Which kind of technical skills? Is this person is going to teach you something (for instance some programming languages)? Or is he going to do the programming part of your PhD project for you and teach you that way?

@Enthusiastic Student: I have a concrete plan as to what I want to represent and analyse in a computer model, i.e. I have defined the algorithm and published a paper on it. I would be asking them to help me 1. analyse the data coming out of this model using e.g. excel 2. represent it on paper in a suitable mathematical representation and 3. help me program it in a number of different langauges for verification (undecided). So, I would be getting technical help with specific things for short periods, not have a permanent employee.

Why are you asking us, and not your Ph.D. supervisor?

@GEdgar I plan to.

@davidCrones That does sound like a bit much "help" for me. Aside from coming up with the algorithm, your tutor would basically help you every step of the way. Most PhD programmes would probably not appreciate this.

@xLeitix: point taken, it sounds like I don't want to do any work. I have a Matlab set of models implemented with basic stats, and want to quickly get better skills in areas I see as making the research better, i.e. more advanced skills in stats, math.

@davidCrones that sounds like the kind of things your supervisor should teach you to learn by yourself.

In principle, as long as you give credit where credit is due, and as long as you do a thesis worth of work yourself, there need not be any problem.  A nice example: many large biosciences have lab-specific technicians or technicians in share core facilities who carry out routine work and protocols.  The student may not be paying them directly, but they are paid to do things for the benefit of the student's work (e.g., mouse colony maintenance, routine DNA preparation, sequencing, etc.) that may end up contributing to a thesis.
The specific examples of work that you want to outsource, however, are rather concerning.  If you are working on computer algorithms, then you should be comfortable with basic data analysis, plotting, and programming.  If you aren't, and need a tutor to help get your skills up to speed, that's fine.  If you're outsourcing simple but non-routine analyses that you should be doing yourself, however, it's likely to introduce serious problems because you will not be in a good position to debug the problems that will arise during analysis.  Furthermore, as a prospective future employer, it would also make me very concerned about your competence in your area of study.
In short: tutoring and outsourcing routine tasks if fine; outsourcing your core work is not.

As mentioned in your comment you are planning to ask help on data analysis and programming.
As you are a PhD student, not a project manager; you should ask your PhD advisor whether those chores are your duties or not. I mean, it may be part of your duty as a PhD student to do data analysis and programming, so asking someone else to do it for you will not be a good idea.
May be your PhD advisor has another PhD student or postdoc in his laboratory or research group and he may ask that person to help or teach you the programming and data analysis methods. He may decide that person to collaborate and do some parts of data analysis/programming for your project. May be he is expecting you to do those duties as part of your PhD programme.
Policies on your program and project also play important role in answering your question. You should make sure whether you are allowed to ask somebody to enter your project (even for short periods) or not.

Is it OK to get external help during your PhD if it is acknowledged?

My answer to your question is, I cannot say whether it is OK or not. It depends on your PhD program, your university/research institute's policies and expectations of your PhD advisers from you.
Of course, learning methods you need to do your project and asking somebody to teach these skills and methods to you is a good idea. You may ask someone to teach you programming or data analysis methods.

As a fellow PhD Candidate myself, here's something else to consider. In my field of study (social sciences) people often hire professional statisticians to run the analysis for their dissertations because they are "people persons" and don't like advanced math. They often want to go into counseling or something like that where knowing how to run a multinomial logistic regression isn't really useful for their day-to-day job. It's understood that this is a wide-spread practice. I, for one, enjoy research and I've made it a point to learn everything I can about the analysis for the simple fact that the analysis will be asked about during my oral defense. If I paid someone to "run the numbers" for me, would I be able to adequately explain what methods they used or what the results mean and why I came to those conclusions? I'd rather take the extra time and do it myself so that I understand every aspect of the analysis. I have seen several people bomb their defense for this reason.

You touch on the major concern that I have with this practice. If I pay someone else to "do the math" and then present the results, how do I even know the results are accurate? Do I understand the underlying assumptions of the methods used by the stats guy? Do I really know how generalizable those results are? And if the answer to these questions is "no", then how can I present and argue for my research results to a critical audience?

That's exactly the point. When doing my dissertation I insist on doing everything myself. Even if I never run another statistical analysis again (which is unlikely in my case), I still wouldn't pay someone else to do the math because they will ask about that at the oral defense. If I don't know or can't answer those questions, it just screams ineptitude and I would fail, in which case everything I've done would have been for naught. I would rather pay someone to teach me how to do it myself.

If your PhD is in computer science or electrical engineering, it is expected that you can implement an algorithm in, say python or C++. Ask your advisor.
Once upon a time, a civil engineering, PhD student, friend told me he had discovered this approximation (optimizing a hill's shape/slope for erosion resistance). He asked me (a physics PhD) if I could help him justify the math in exchange for being the middle author. I agreed and spent 10s of hours learning about continuum mechanics, programming a boundary value problem, deriving math, and proofreading the draft. Everyone was very happy with the collaboration.


text:
Is it appropriate to call a professor for a recommendation on the weekend?
I emailed my professor about two weeks ago, but there was no response to my first email. I sent a follow up, and got a reply saying they'd be happy to write one for me on the following weekend. I waited, the weekend passed, and nothing happened. I followed up  again, and again no response to my email.
Now I am thinking to call as a reminder. My professor has written many recommendations on my behalf, and my guess is that it didn't get done  due to  laziness or  forgetfulness. Now we have a long holiday coming for the next ten days and I want a recommendation as soon as possible. Is it appropriate to call  on the weekend given the fact that it was said that it could be written one a previous weekend?

Your guess is that "he is lazy"? You hardly make it sound like you deserve "the guy"'s recommendation. How can a [tag:etiquette] question be so disrespectful?!

Did you try visiting his office?

I never meant to be disrespectful. I actually have a lot of respect for him. I am sorry it sounded disrespectful.
We are in a long holiday now. If I don't hear from him then I will visit.

@OllieFord Your comment strikes me as an overreaction. Why is the guess that "he is lazy or that he forgot" disrespectful? Regardless of whether the OP deserves a letter or not, Is it really unthinkable that professors can be lazy? Frankly, repeated negligence to reply to emails is more rude than making an (unjustified) guess.

@Drecate I view this question with great distaste. I cannot stand the sense of entitlement in OP's language; let us not forget that he [was] asking for a favour.

No -- it's totally inappropriate.

Seriously. Think about it. Unless you're at a school where profs phone grad students at their home on weekends to inquire about a late paper, it's totally inappropriate.

Note: Many grant agencies / admissions committees know that we (the faculty) are thorough flakes and couldn't be trusted to tie our own shoelaces in the morning. They usually give a few days of extra time for faculty references to come in after the deadline.  Others, however, are very strict on deadlines and thus faculty need to be properly shepherded into getting their materials in time.

+1 - although this brings to mind a recent Friday evening, around 10pm, when a new Ph.D. student, discussing the latest paper at our kitchen table, watched in horror as her professor matter-of-factly called a more senior Ph.D. student of hers to inquire about some data - which second Ph.D. student, at a BBQ, just as matter-of-factly provided the requested information off the top of her head. Did I mention it was a Friday evening, 10pm? Nice to see other people have other working hours, though. ;-)

Do as I say, not as I do. Power has its privileges. There's always one exception to the rule. Etc etc. O:-)

That's good advice, Chris.

One thing that I've noticed with my better-prepared students is that they tell me about the deadline 2 months ahead of time, then 'ping' me 1 month ahead, 3 weeks ahead, and 2 weeks ahead of the deadline. They then escalate warnings quite incessantly after that point. Maybe it's because I've trained them quite well that I'm not to be trusted, but they take it UPON THEMSELVES TO MAKE SURE THAT THE FACULTY MEMBER DOES THEIR JOB. Sorry for the shouting, but if a student only checks the application website the day before the deadline, that's way too late.

You need to be constantly aware and alert and give profs a lot of lead time as well as plenty of warnings.

@RoboKaren: So, if you're at a school where profs don't call their grads at home on weekends then it's totally inappropriate by principle of reciprocity. Whereas if you're at a school where profs do exactly that then it's totally inappropriate by "do as I say not as I do". I can't help feel your answer comes to the correct conclusion by a faulty argument :-) Realpolitik is that it's inappropriate because the prof can forbid it, and most people capable of forbidding it would do so regardless of whether they take advantage of the fact their students cannot forbid it. Power corrupts!

The principle is this: it is rude and boorish to call work related people at home on evenings and weekends with work related business, unless there is a critical and unforeseen emergency. Some faculty by virtue of corruption by power or personality, are rude and boorish and ignore this principle viz a viz their grad students.

If you are going to call on a weekend, call his office phone and leave a message there. Then he can check the voicemail if he chooses to.
When following up on these things, it is always good idea to ask if you can provide any additional information.
Btw, keep in mind, you can express your concern with the delay of your letter, remind them of the deadline, and offer to provide information. But you cannot require it done this weekend. This person is doing you a favor and nothing obliges them to write one for you this weekend, or ever again.

Not to mention that if they are the type that doesn't check their e-mail on the weekend, then they are also the type that doesn't do administrative work on the weekends either. It can wait until Monday.

No.  In the cultures and universities I'm familiar with, it is never appropriate to call your professor's personal or mobile phone.  It would be very unusual even to call his/her office phone.
And if you ask in person instead of by email (in the first place) you're more likely to get what you want.  You're asking a busy person to devote a significant amount of time and attention to do you a favor, with no compensation.  In most cultures, asking in person shows that it's important.

Wait, what is the purpose of the office phone if you cannot phone it? My boss phoned me on my mobile quite couple of times during my holidays or other times when some project deadline was in danger and he needed some credentials or anything I think I had to do the same at least once. I wouldn't recommend to do that in this case, of course, but you cannot even call the office phone in an important issue?

Lots of people call me on my office phone.  But my students do not.  I also don't call my students on the phone, so we are probably operating in different cultures.

I disagree on the office phone bit -- even though my voice mail says to not leave a message but to e-mail me. Office phones are fine for office business including student business.

Perhaps it's just that my students know that's the slowest way to get a hold of me (and I knew the same about my advisor, so I never called his phone even once in 5 years).  If I'm in the office, they can knock on the door.   If I'm not, I won't be able to answer my office phone.

@VladimirF Calling a landline phone does not give you the luxury of knowing whether the person you're interrupting can talk at that moment. How do you know they're not very busy, or in a meeting?

@Moriarty: If they are not able to talk, they will either not pick up the phone or answer quickly to say they have no time to talk.

Actually, both places where I've been (PhD and postdoc, different countries in Europe), it was quite common to exchange phone numbers when going to conferences between all students, postdocs and faculty, to make people free to attend sessions which they chose but then be able to coordinate meeting up for lunch/dinner/social (where quite often all team members attending the event come together). Not a similar situation at all, just an example how "never appropriate" might not be exactly true in all cultures

On the converse. I once had a professor be relatively upset that I didn't call, after finding myself last second in a tough spot. There is an appropriate time and place to call, and some professors will be more okay with it than others, but I would only suggest you go through with it if they know you well.

As to professionalism, in the real world would you phone your boss on a weekend to remind him that he did not do something that he was supposed to do (such as email HR on your transfer)? No, you'd wait until Monday.

Well based on your past experiences you know your professor better. One of mine does miss many of my emails and another responds even at night or on holidays. So it's probably more of a habitual thing (considering most professors are busy but not all respond late) than ignoring you specifically for some reasons.
A reason for delay might be that he forgot your credentials and needed some time to look at those again, to write a more accurate recommendation.
A suggestion I would like to make though, use a mode of communication that this professor likes more (mine likes skype and responds quickly on those messages).

If he knew the prof well enough to phone him regularly, he wouldn't be asking this question.

This guy wrote many recommendation on my behalf seems to me as knowing the professor well and vice versa

My professors don't mind if I ping them on weekends, they may choose not to respond occasionally, but never mind, you may have a different opinion @RoboKaren

Ping with an e-mail is different from phoning their homes.  I've written over 50 letters for a student, but the only reason they'd have to phone me at my home number on a weekend is .... I really can't imagine one other than they are coming to my house for our annual dinner and they are lost or don't know what to bring.

I think I mentioned use of mode of communication that this professor likes more. Not all of them are allergic to phone calls. And a skype call or similar can get the job done for OP, he doesn't need a phone call necessarily.
Well we agree to disagree if you are not convinced this time.

The OP uses the word "call" in can I "call the professor?" Your short answer "yes" is in reference to this original wording.

When in doubt: no. But it depends on the teacher. And often fortune favors the bold and the brave. If you can get away with it, and it helps you get the recommendation, why not?
"Professionalism" is still secondary to results. Besides, if you have his cell number it is already a kind of permission. I mean it, you should only have gotten it to use it. Go for it, apologize for calling on the weekend to keep connected, proceed to give nothing but a gentle reminder (of your deadline/how nervous you are about getting all the documents together), that's it. Won't hurt either of you.

-1 This is the worst advice I've read on this site. I give my TAs my cell number so that if there is an emergency (student has to be taken to the hospital, building is on fire, etc.) they can contact me. However, calling me for a non-emergency (and this is entirely a non-emergency) will only get me pissed and wondering about your professionalism -- at a moment when you're asking me to comment about your qualifications for a job/position/acceptance.

p.s. Fortune favors the bold is what drill sergeants tell new recruits so that they will willingly go into a minefield to try to attack a well-protected machine gun nest.

You also give your cell phone number to a pizza guy in case he gets lost bringing you pizza. But, would you appreciate out-of-blue weekend phone calls from him?

Well, I guess only the OP can tell us why he has the phone number. I'm not sure why people are so unhappy about calls and so happy about e-mail. E-mail was attempted and failed, what more is there to do? What's really unprofessional is not doing as you said you would. Being called in response to that.. Well. Think of it what you will. (nb: I'm not sure these sort of questions are appropriate for the stackexchange format. In my world my answer is correct. StackExchange users are not a good statistical source of what's correct. It's just weird to use votes as "I agree" or "I disagree".)

@RoboKaren, Do you think it has to do with being an anthropology professor at a private institution? I don't suppose results really matter in that field. It's always more of an appreciation for things than a proof of this or that, in my experience. I'm genuinely interested in why it's "unprofessional" and gets you "pissed".

Good question, Lod. If I was part of a lab group, I might welcome phone calls more, especially of the, "all the chimps have inhaled a super secret virus and broken out of their cages," variety. If I was at a public school and had more students, I think I would be protective even more of my family time on weekends - and try to instill even more professionalism on the party of my larger cohort of advisees.

As to why it's unprofessional, in the real world would you phone your boss on a weekend to remind him to send that note to HR about your transfer request? No, you'd send a tickler email and/or remind him on Monday in person.

Depends, to be honest. Why wouldn't I? If it can speed things along, I would. And he'd be happy I reminded him, and that I think his opinion is so important. If there's no urgency I wouldn't call.

Good luck in either the real world or academia, Lod.

authors: Vladimir F Героям слава


text:
Why are small distractions impacting my day so much?
During the pandemic, at least the premier institutes of my country are operating in work from home mode. Since this lessens the physical activity of going around labs and classrooms daily I tried to setup a fixed timetable and working environment for myself to do learning and research and was successful in doing so.
But over time, I observed the following phenomenon

Utilizing the day (fruitfully) to full extent if and only if there is
no distraction. Distractions include very small tasks including
meeting colleagues outside home and spending few minutes with them. Phone conversations with supervisor etc.

I am surprised to learn that my whole day becomes under-utilized if distraction happens during early parts of my day. And I am not in a position to know the exact reason behind it. Ideally, I need to break only a few minutes from my timetable and can utilize the remaining time. To my surprise, it is not happening. Either I am spending my time randomly or I am unable to properly concentrate on my work. This phenomenon generally did not happen or happened only to a very minute extent during non-pandemic days.
Is this phenomenon normal or do I need to completely prevent/avoid distractions?

You never had distractions before working at home? What about emails? I improved my work a lot, the day I realised I could turn off my email client.

What happens if you ignore your phone and email during those early parts of your day?

Maybe off base, but perhaps talk to a psychiatrist? ADHD is more common than many people realize, and today's medicines for it are much better than even those from a decade ago.

Not really suitable for this site, in my opinion.

Are you sure that you want to ask this here? Might not our life hacks sister site be more appropriate?

@JonathanLandrum: As someone with ADHD, that was my guess too. A therapist and/or psychiatrist would probably be better able to assess the matter.

Distractions are a tax on productivity, because you lose much more time than the duration of the distraction. It takes a lot of time and energy to switch between tasks and to regain focus. Apparently, you need on average 25 minutes to regain deep focus after becoming distracted. If you work four hours in the mornings and are distracted four times for five minutes each, half of your working time is lost before lunch break ((5 minutes + 25 minutes) * 4 = 2 hours). This also applies to self-interruptions, therefore multitasking makes you less efficient.

Is this article talking about the Pomodoro method without naming it? I have experienced great benefit from structuring days around implementing this method for focus.

@Darla It's a bit weird that the pomodoro technique recommends a break just when the focus is fully developed. Perhaps that means the break should be a real break (stand up, take a few deep breaths, go outside...) rather than a distraction (twitter, email), so it's easier to go back into focus.

@henning You just validated me and my experience with pomodoro! I've been keeping track of my time during the pandemic and trying my best to do 25 min on / 5 min off, but it feels like I get "into my zone" just when the timer ends! But I have heard so many people say pomodoro is the be-all-end-all of productivity, and so I end up following pomodoro like I'm told and feeling bad that maybe I'm the one who's flawed to make pomodoro work. Turns out I should do whatever works for me!

This 25 minute discussion sounds misleading. It seems to come from this paper, which says "When  people  did  resume  work  on  the  same  day,  it  took  an average  length  of  time  of  25  min.  26  sec. (sd=54  min.  48 sec.).  This may seem like a relatively short amount of time, but it is also important to consider that before resuming work, our informants worked in an average of 2.26 (sd=2.79) working spheres. Thus, people’s attention was directed to multiple other topics before resuming work.". Not ideal, but not entirely "lost" either.

I love how the people complaining about the Pomodero Technique are the people who have slavishly followed it to the letter, instead of understanding that it's suggestions that you should adapt to make work for you. Very similar to how the Agile Manifesto is widely, and incorrectly, hated in software development!

@Ian Kemp, yes I think the 25 minutes are not the point, but rather the idea of periodization. It makes you less scared to get going (helps against procrastination) and ensures that you take enough breaks. When writing up my dissertation, I often committed to 3x25 minutes and ended up doing 3-4 x 60 minutes, with a longer break after the third repetition. There's no point in interrupting yourself when you're being focused (but beware the unrecognized energy drain). On the other hand, I've heard five-minute intervals being suggested for heavy procrastinators with strong task-related anxiety.

The issue you're experiencing is the problem of context switching. Multitasking can result in a 40% productivity cost, make tasks take 50% longer, and increase errors. After an interruption it can take ~25 minutes to regain focus. (It's hard to find good citations for these numbers, unfortunately.)
The solution to your problem is to guard your time.

Determine what priority you should assign to what you need to do. Consider using the Ivy Lee method.
Turn off buzzers, ringers, alert sounds, and dialog messages. These interrupt periods of focus. Leaving alerts on implicitly places others' prioritization of your time above your own. If you don't manage your devices they will manage you.
Consider using something like the Pomodoro technique or similar strategies to interleave focused time with breaks and outside communication. While scheduling a whole day might be hard, committing to doing something without interruption for 30 minutes is something you must be able to do to get anything done.
Try to understand where your tasks fall in the time management quadrants and value/prioritize them accordingly:

I am always intrigued by the difference between the first and second quadrants, or rather, how to prioritize them. After all, everything that's in the second quadrant becomes urgent and moves to the first if you don't schedule enough regular time for it.

Do the quadrants above originate from (or are adapted from) Stephen Covey's work? Just wondering, as that's where I first seem to recall having seen them.

@henning: On its face, the difference between quadrants I and II seems simple: the things in quadrant II are important, but they don't have to be dealt with right now. It's enough to deal with them when you don't have any quadrant I issues at hand. Of course, as you note, putting off many quadrant II things for too long will move them to quadrant I and/or have other negative effects on your quality of life, relationships and mental and physical health. […]

[…] The real problem is when you find yourself always having quadrant I things to deal with. That's a sign of chronic stress overload, and often requires (sometimes painfully) re-evaluating your life situation (and possibly your boundary between quadrants I and III) before you end up burning yourself out.

@IlmariKaronen This being academia.stackexchange, it is worth pointing out that for PI positions, top level research lies in quadrant II. Thinking about something a lot, and having a bunch of insights, cannot be done at the last minute. So it never "becomes urgent and moves to quadrant I". This, not quadrant I, is what you will be evaluated on for tenure/promotion/grants etc., and if you spend all your time answering the urgent emails of students and staff and random people, your research will get left behind and your career will stall.

While the pomodoro technique and the urgent/important priorisation has already been mentioned, here's my personal suggestion, which includes both of them in some form or fashion:

If you don't already have it, use an acceptable calendar app, shared between your PC and smartphone, one that integrates well with your mail system and whatever your colleagues are using.
Meetings will be in the calendar anyways, probably.
Now start putting everything in there. Especially if you intend to work alone on a topic, be sure to block that out. Don't forget break times (lunch etc.) -  enter them as well.
At the beginning of each day, check your calendar for today (this will also be your first calendar entry each day - "Clean up today's calendar"). Look for all conflicts and resolve them by moving them around, maybe cancelling invitations or not so important events. Here, the urgent/important distinction becomes important, of course. Your calendar for today should now be completely filled. Not only with work - there will and should be breaks in there as well, but they should be there explicitly.
Configure your system so that mails do not pop up notifications, but your calendar does.
Now comes the hard part: when your calendar tells you to switch to another topic, do it religiously. If you have not finished your current work, immediately find a new time slot (tomorrow or maybe today if there is another event which is not so highly prioritized) and plan it in there.
When your 8 hours per day are up, or however much it is, stop working. Don't fall into the trap of doing everything that fell on the wayside during the day at the end.

Over time, this trains you to be methodical and realistic. If you notice that your time slots regularly are too short, then you might have to fine tune the size of those slots (for me, that's usually 30-60 minutes; 120 minutes very seldomly), or reduce the content you put in there. You want this to be a game: being done with what you intended to do in a slot should give you a little spike of joy.
You can and probably should, at least at the beginning, have buffer time slots; i.e. plan in an hour a day (or maybe one in the late morning, one in late afternoon) as a pure buffer. As you get used to it, this might not be so necessary anymore. If you run out of stuff to do in a buffer, do whatever - either take a walk, or pick anything else you wanted to do later, and pull it forward.
Reading your mail is an activity like any other - put in a time slot for it, and if possible avoid checking your mail all the time or at least ignore mails coming in during the day as best as you can (you might still look there to get updates on the things you are workin on right now).


text:
Professor reviews proposal as a favor, should I send a reminder
I am applying for PhD, and in the application I am required to write a research proposal.
I asked my thesis supervisor to write a recommendation for me, and he agreed,but he told me that I need to work more on my writing and carefully write my research proposal. He told me to have people read for me before submitting it and suggested that I send it to him so he can review it for me as a favor.
I got his email with feedback on the proposal. In the email he wrote "Here is my first feedback." We discussed the review he made and I made changes and he asked me to send him the new proposal. After I sent the email, he told me that he will read it and give me another feedback that same night. That was about five days ago and now he is on a vacation.
Would it be appropriate to remind him ? I need his feedback because I am trying to submit the application. Should I just submit the application and just assume that he is too busy for me ? I don't want to be naggy and annoying. After all, he is doing me a favor.

You are seeking an advice on how to communicate with your thesis supervisor. The only one who knows the guy here and is you.

Send an email suggesting you don't assume he will offer any more help, but leaving the door open in case he offers some:

Thanks so much for your help with my proposal. I believe your suggestions have really improved it. Attached is my current version; I will submit it tomorrow evening. Let me know if you have any last-minute suggestions before then.

Thank a lot. Smart and simple. I will do that. If I don't hear from him I will proceed and submit.


text:
I found a mistake in my master thesis's code
I defended my master thesis couple months ago in a German University. It's a thesis in Computer Science. In my thesis I mainly implemented some machine learning methods and compared their performance. The implementations of the methods and making them available as open-source are considered one of the main contributions of my thesis. I published the source-code online on Google's Code.
However, recently I was browsing the source-code of two methods' implementation and I found two bugs. One of the bugs makes the results of one experiment useless since the method became simply wrong.
Now I'm very worried about that and don't know what to do or what I must or have to do. (They're not going to take my certificate back, right?)
My questions:

Since one of the main contributions of the thesis is the release of the source-code, am I obligated to fix the bugs?
Am I required to keep my source-code online? In other words, can I now decide to take it down and not give it to anyone? I'm the only one who has a copy of the source-code. My professor never asked me to put the source-code on a CD-ROM and put it in the thesis. I also mention in my thesis the online repository for the code.
I had very difficult memories of academia and I was so relieved when I finished. I don't want to contact them again to tell them about the bugs. But am I obligated to do that? I just want to start a new life and never think again about the past.

I'm asking those questions just to know my rights and if I have any obligations. However, since I'm passionate about my thesis topic, I'm actually considering fixing the bugs but I'm not willing to contact my professor and tell him, simply because I just don't want to communicate with someone from the past and still feel that I'm still stuck with academia or have obligations toward them.
Nobody has used my code yet, so if I fix the bug then the person who will clone the project will get a correct version (hopefully! I mean every software is subject to bugs!).
Edit:
I was asked "obligated by whom?". Well what I'm thinking is that since one of the main contributions of my thesis is the source-code, and since my examiners passed my thesis because it has contributions, then I thought that I must have that source-code always available. It feels to me like a contract:
Make contributions (source-code as the main contribution) -> thesis passed -> you get your degree.
Now revoke contribution -> thesis failed -> you don't deserve your degree.
Isn't it like that?

Relax, nobody's going to care about a bug. In the end it's just a master thesis. You won't lose your degree.

Hopefully, you included the commit SHA-1, instead of just saying "this repo" when you were referencing things in your thesis.  This way, everything in your thesis will still make sense.  If you make a new commit with the message "This was broken, is now fixed, invalidates chapter 2 of thesis because blah", I think that would be a good thing.  I do not think your degree is at risk, and I do not think you are obligated to report to anyone.

The idea of you passing your thesis is not that you made a correct solution, but rather that you could work through the problem in a systematic way.

Just a thought, you if you've uploaded your code online, why not commit an updated revision whenever you have some time? You don't have to remove the original file, rush it or inform anyone that you've fixed some bugs, and the updated code may produce different results from the ones you've published. However, if anyone ever wants to use or see your code for whatever reason, they'll quickly see there was an update, which in my opinion will save their time figuring out wh the results are wrong, as well as give you some credibility points.

I think that you have some misconceptions about what a thesis is and what a degree is.  A thesis is not a contract, and your future obligations upon obtaining a degree are precisely zero.  It is not an honor that can be revoked for later conduct unbecoming: rather it is a permanent recognition of your past work.
A thesis does not even have to be completely correct.  I feel a bit like the guy who's telling you the truth about Santa Claus, but a substantial percentage of theses are approved by committee members who know they are not completely correct.  The judgment is rather that they are good enough to meet the committee's standard.  A thesis which turns out to fall through completely based on the writer's honest mistake would not be revoked (well, in our wide, wild world many strange things can happen, but I've never seen this).  The fault here lies with the committee: they are supposed to be experts.  Moreover the thesis is not awarded because the work is a service to the community but rather because it was judged that the candidate demonstrated sufficient mastery by doing it.  In fact it is possible to demonstrate this mastery even through flawed work, sometimes even through work which is so flawed that nothing positive can be extracted from it.  In my experience the only reason for withdrawing a thesis is fraudulent activity done by the candidate in the process of the thesis work.
So yes, in my opinion you could take down your open source code without any realistic fear that your degree will be revoked.  Should you?  I don't think so: in my opinion that would be very immature.
A master's thesis is a professional degree.  In other words it's a kind of adult degree, and anyone who has one should be ready to act like an adult.  Only with difficulty am I restraining myself from launching into a psychological analysis of the levels of moral reasoning on display here, but I find it interesting that your entirely irrational fear of retribution seems to be saving you from doing the wrong thing. If you said that you would make something available then pulling it now for purely selfish reasons is...um....no, I had it before: purely selfish.  To justify your behavior you write

I had very harsh memories in Academia and I was so relieved that I finished. I don't want to contact them again to tell them about the bugs. But am I obligated to do that? I just want to start a new life and never think again about the past.

Fact check: this all started with your reflection on your past work.  If you want to start a new life and never think again about the past: okay, do that.  Never thinking about the past does not include tampering with the presentation of your thesis work. (By the way, such tampering could certainly earn you some future contact by those who want to see the work and want to know why you took it down.)

However, since I'm passionate about my thesis topic, I'm actually considering fixing the bugs but I'm not willing to contact my professor and tell him, simply because I just don't want to communicate with someone from the past and still feel that I'm still stuck with academia or have obligations toward them.

It's pretty clear that you have not moved on, in both positive and negative ways.  Again you have some strangely childlike ideas: once you leave academia, what obligations do you have to your professor?  Precisely none. But "I'm not willing to communicate with someone from the past" is not a professional attitude.  (I am aware that in real life professionals can behave very badly.  Professionalism is something that professionals aspire to, not always successfully.)  What about future students who will try to continue your work?  Don't you care about them?
In summary: yes, you are absolutely allowed to behave completely selfishly in this matter, acting to prevent your future embarrassment and evade any unpleasant memories.  But try to rise above.

they're not gonna take my certificate back, right

No, your degree won't be revoked on the basis of an honest mistake.  (Revoking the degree would only make sense for serious fraud or misconduct.)

Since one of the main contributions of the thesis is the release of the source-code, am I obligated to fix the bugs?

Obligated by whom?  There's certainly no legal obligation, but deliberately withholding knowledge from the rest of the world would be unpleasant and harmful.
If you know how to fix the bugs without much effort, then I'd recommend that you do so.  If you don't know how to fix them or it would take too much time, you could at least attach a note explaining the problem (for the benefit of anyone who wants to use the code in the future).

Am I required to keep my source-code online? In other words, can I now decide to take it down and not give it to anyone?

Again, required by whom?  Nobody can punish you if you take it down, but going out of your way to deny access is at least unfriendly.  If your thesis said that the code would be publicly available, then changing your mind now would be unethical.

I don't want to contact them again to tell them about the bugs. But am I obligated to do that?

Nobody can make you, but it would be nice.  Think about it this way: another student might begin a project related to your thesis.  If you don't tell your advisor that the results of one experiment were wrong, then this student might experience pain and wasted time that could have been avoided if they had known about the problem earlier.  You might not care about your advisor, but surely there's some value to preventing future students from suffering unnecessarily.
And what's the worst case scenario if you tell your advisor?  Maybe your advisor would insult you, in which case you can take some satisfaction in having behaved better than your advisor, but there's nothing he/she can do to disrupt your life now.
In response to the edit:

Well what I'm thinking is that since one of the main contributions of my thesis is the source-code, and since my examiners passed my thesis because it has contributions, then I thought that I must have that source-code always available. It feels to me like a contract:

If you said in the thesis that the code would be available in a public repository, then you have an ethical obligation to keep it available.  But universities revoke degrees only very rarely and for exceptionally serious reasons, such as research fraud or cheating.  There's no way a university would even try to revoke your degree for taking down the source code.  (However, if you're still worried you could look up your university's procedures for revoking degrees or search online for degrees revoked in the past.)
I don't mean to encourage you to take the code down, and I don't think you should.  My point is that this is about doing what you feel is right (keeping promises, helping other people, contributing to the world's knowledge) rather than about what someone else might try to make you do.

See edit please.


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What is meant by "offers accepted" in Mathjobs portal?
In the Mathjobs portal, some post doctoral positions in mathematics have "offers accepted" written in the post, see:

I am struggling to understand what this means? Because the position seems to still be open and yet it is mentioned that offers are accepted.

Given that the posting provided is for a post-doc starting in August 2024 (a.k.a. last month)*, I think it is safe to assume that they mean exactly that an offer has been made to a candidate and they have accepted the offer (and have probably started the position).
Why the advert on MathJobs is kept open? No clue.
*The statement that "Review of applications will begin on December 15, 2024" is presumably a typo and should say "2023".

I wonder if they tried to reuse their 2023-2024 ad for the 2024-2025 cycle and forgot to update some things.

I am not familiar with the customs on Mathjobs, but it is also possible that someone accepted an offer but agreed to postpone the starting date. This would explain the wording and the fact that the job posting has not been taken off yet, because it is still possible that they will need to fall back to other candidates.


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Thesis writing style: when to italicize?
In a thesis or journal you write all sentences yourself, but on some occasions you prefer to take a piece of text from another source. If you do, should you use quotation marks only, or italicize it, or use both, to identify that you have not written it?
Example for quoting directly from a source:

This can, according to Someone et al. [1], be seen as "an excellent way of representing a piece of text quoted from another
  source", and therefore it's emphasized.
This can, according to Someone et al. [1], be seen as "an excellent way of representing a piece of text quoted from another
  source", and therefore it's emphasized.
This can, according to Someone et al. [1], be seen as an excellent way of representing a piece of text quoted from another
  source, and therefore it's emphasized.

Example for a definition with a source:

Wikipedia defines italic as "a semi-cursive, slightly sloped style of handwriting and calligraphy that was developed during the
  Renaissance in Italy" [2].
Wikipedia defines italic as "a semi-cursive, slightly sloped style of handwriting and calligraphy that was developed during the
  Renaissance in Italy" [2].
Wikipedia defines italic as a semi-cursive, slightly sloped style of handwriting and calligraphy that was developed during the
  Renaissance in Italy [2].

Are there are any style guides or recommendations that refer to italicized text, for either quotes or definitions? And related to the two examples, what is the recommended way to distinguish between a quote and a definition?
Edit: note that if a style guide is provided, the guide should be followed. This question relates to situations where no style guide is required.

FYI: How To Use Italics (wikiHow)

There can be specific exceptions for journals, which may have conventions preserved unchanged from the past, but the general principle is to be typographically simple while conveying the necessary information. Quotation marks are required to unambiguously indicate that a certain sequence of text is a literal quotation; the quote itself should then not modify the format of the text, thus should be roman when the original is roman, italic when it is italic, and so on. Thus, your first option would be the correct choice.

While quoting verbatim from a source, you should always use quotation marks. Italics are generally used for the following purposes:

titles of books, periodicals, blogs
genera, species, and varietes
introduction of a new technical term
letters used as statistical symbols or algebraic variables
some test scores and scales
periodical volume numbers in reference lists

If you have used quotation marks to indicate that you have borrowed the text, I do not see any need to italicize it. Style guides also advise against the use of italics for mere emphasis. Hence, it is better to use quotation marks only to distinguish text that you are using verbatim from another work.

"introduction of a new technical term"
So, that term will always be italic? or It should only be italic once it's introduced first?

I agree with User6726’s answer, but want to add a few things.
For a journal publication (to make the answer more general) you could check the journal’s style guide or how italic type is used within articles published in the journal.
As your question is specifically about a thesis, find out which style your thesis should be in (APA, Chicago, etc.). You will be needing this information for formatting your references anyway. With this information, check online or in your library for a a style manual for the specific style. This manual will explain when italics are appropriate.

Our university does not require a specific thesis style, so I'm 'creating my own'. So my question maybe relates more to 'general' writing practice.

In that case, to make your job more easy and because most academics prefere consistancy, I would ask either your supervisor or your the 'head of your program' if there is a style they prefer and stick to it. Or, if you don't want to bother them with this, choose and stick to an existing style yourself

You probably choose some template (class) for your thesis. This template may be associated with some style. If not explicitly, then by how others are using it or where it comes from.

Italics are used for emphasis. Use sparingly, where required by custom (biologists write species in italics, I believe), to highlight a new term being introduced, and precious little else.


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Is it worth pointing out missed works in already published papers?
I have come across several works that omitted the citation of relevant related literature, but clearly are camera-ready versions already accepted/presented at a conference or journal.
Of course, due to the familiarity, these missing works may include some of my own papers, but for the sake of this argument, it should be assumed that they may also include the work of others.
What is the general expectation on discussing such omissions with authors?
Is it recommended to reach out to the authors post-publication and point out to them which resources/related literature they "missed" (IMO)?
I also want to add that I presume the omission is usually in good faith, i.e., simply because of the lesser popularity of these methods.
As the answer may depend on the field as well, I am active in the area of Computer Science, which tends to have a comparatively high publication turnover.

Great ! Not only is everyone a football trainer now, but everyone is also a referee!

@Oбжорoв: I don't understand your football metaphor. Most scientists actually do have relevant experience with reviewing papers in peer review.

Is it recommended to reach out to the authors post-publication... - I don't think there's a general expectation.  It matters is how relevant they are, and whether you think the authors don't know/understand those references, and would benefit from them.

I wonder what you expect will happen after? If you mostly want to inform authors about other relevant earlier work, that's fine (particularly if you are not talking about your own work), but I doubt that papers are regularly errata'ed simply to cite some additional earlier work. For the latter there would need to be some actual misconduct, not just "there are some more related works you haven't discussed".

@xLeitix I agree, the expectation is not to fix errata in the published pre-print. But rather my intent was to expand the awareness of the authors for potential future work. In case that relevant applications (or conflicting approaches) are missed, it may help future study design or evaluation.

I really think that a lot of the answers/comments here while correct as written, are really missing the mark in flavor, it depends on how you write that email. I have expanded in my answer below. The focus should be on collaboration and shared interest, do not point out the omission, the authors can infer that on their own, its their judgment to make.

It depends on how you do it. If you say,

I really enjoyed your paper on X. We have some lesser-known related
work Y (attached). Its cool that you found result Z we found result W which is similar but also differs in some ways. It would be great to have a chat about our common interests.
Would you be open to a zoom meeting?

That is totally fine. You should not mention that they didn't cite you. Just focus on actually advancing good research. If they like the work that you point out in this email, they will likely cite your papers in the future, now that they are aware of them. You might learn a bunch from each other and get a collaboration going.
If you say

I noticed you missed a citation to my work X in your recent paper. Let me explain...

No, that will be bad for your career. Nothing comes of that. You will look petty, and you could kill a potential collaboration before it ever starts.
Note in my proposed method you aren't pointing out the missed citation explicitly, but you are very very subtly suggesting it. No reasonable receiver of that email would think you were asking for a citation, but it's your best chance of potentially achieving that outcome in the future. If you point it out explicitly it will just annoy them.

If by "worth pointing out" you mean feeling good, then yes. If you mean advancing your career, then no.
I would welcome an email pointing out that I missed an important citation. But if the email is from the author saying that I did not cite them, I'd probably be more annoyed than pleased. And if it's some nit-picky stuff, e.g. I only cited 5 of the 6 relevant works, I'd make a mental mark that the person sending the email is a nutcase with too much time.
Authors have wide discretion regarding citation. I don't like ceremonial citation, even though it is very common in my field, and that's my prerogative  (ceremonial citation is citing the same old papers because it's what everybody does, regardless if the paper is relevant to the sentence preceding the citation.)
So before you send an email to an author pointing out that they missed an important citation, double check that the citation is germane to the topic, the omission is crucial to the argument being made (ie did not cite a paper countering the argument), and that your motivations are to inform the author rather than recriminate why they didn't cite you.

Noone is required to cite works that they do not refer to - if not using certain papers as a reference, they are not (necessarily) omitted, just not used. If there are 20 papers relevant to my research, but I manage to say what I need to say by refering only to 10 of them, the others are not "omitted" but simply not necessary. I don't really understand the problem. If I were contacted by someone asking me to next time cite their paper, I would probably perceive that as spam or coercion.

Also moving my previous comment: In the instances I refer to, it may not just be a trivial omission of relevant work (e.g., missing in a citation like [1,2,3,4,5]), but rather a central approach to a problem that is tackled in the specified work. I understand that the notion of what is "central" is different, and your response clearly shows the ambivalence that people have towards this topic.

Papers are generally expected to discuss their place among the state-of-the-art, establishing what the paper is adding. This typically requires discussing (and therefore citing) related work.

@TimRias But not sufficiently contrasting to earlier work is a paper quality issue, not misconduct. Once a paper is accepted, it is accepted "as is" aside from actual factual errors, misconduct, etc.

@xLeitix Who is talking about misconduct?

@TimRias Nobody is talking about NOT citing related work, just about not citing specific papers.

The question is specifically about not citing relevant related work.

If you think the authors have missed a potentially successful approach, don't beat around the bush pointing out papers that they could have cited, just ask them straight out.

@TimRiad The question seems to be about not citing a set of particular papers, instead of not citing any related work at all. It's perfectly possible to present the state-of-the-art accurately without citing every single paper it consists of.

It depends on how relevant the related literature is.
If it's close enough that it might raise questions of priority, for example, a simultaneous invention, the authors certainly should know about it. There's a palette of actions that they might take, for example, updating the preprint version of the paper with a pointer to your paper, and acknowledging your paper in talks.
If it's only "some" related paper that does not affect questions of priority, it's wiser to let it slide. Authors generally don't have an obligation to cite all works that are, to some extent, relevant and related, as it would in many cases lead to an overly long related work discussion with little added benefit, basically a full "survey paper within a paper". Approaching them about it could come off as somewhat desperate.


text:
Does it look bad to get recommendation letters all from the outside of undergrad school?
I'm applying for Mathematics MS degree and I have an issue with getting an recommendation letter from undergrad professors. I didn't plan to apply for grad school unitil recently and I was never a type of student who visits professors during office hour or get friendly with them. Fortunately, I know two professors that I've worked with during an internship and they are willing to write me the letters. But as most schools require three letters, I still have an issue.
I do have classes (semester-long) that I got good grade, but again, I've never talked to any of those professors. For now, it seems I have two scenarios.

Get letter from someone from non-academic field that knows me personally
Get letter from undergrad professor who doesn't know me personally

I know it sounds ridiculous, but what would be the better choice?
Thank you.

Get a letter from an undergrad professor that you got a good grade from, preferably in a smaller-size class. That letter won't be weighted very heavily, but it won't raise any red flags, the way that having no recommendation letters from your undergrad coursework and one non-academic letter might.

A "did well in class" letter is not helpful but is better than nothing.

@PeterShor What is this mythical “smaller size class” of which you speak?

@JeffE: A professor with a student in a 1000-person class is probably less likely to be able to say anything about a particular student than a professor in a 100-person class, and of course, a 30-person class would be even better. If the only classes the OP has gotten good grades in are 500-student classes, they may be out of luck.

@PeterShor My point is that in many degree programs (like mine), students may never have a class with less than 100 students. — I was never a type of student who visits professors during office hour — Note to future readers: Do not do this.

@JeffE: Note that I said smaller, not small. I've written letters for students who took 80-student classes with me. I expect they weren't weighted that heavily by the admissions committee, but for graduate admissions,  I still think they would be better than a random person outside of academia, even one who knows the student well.

I would recommend getting a letter from someone in the field even if they do not know you personally, but this is based off of my experience from getting letters and may vary slightly from what you are doing. The guidelines I was given were to obtain letters from 1) someone who is able to speak to my academic talent and 2) someone who knows about the program you are applying to. In this instance, it would be helpful to get a letter from a professor where you did well in their class. If you need letters for other purposes (like a character reference), then it may be helpful to consider getting a letter from someone who knows you personally. If you get a letter from someone who has never gone to grad school, it may be difficult for them to explain why you would be a good candidate for the program you are applying to.
Even though you did not spend a lot of time getting to know your professors, you would be surprised at how many may remember you. I faced a similar dilemma when obtaining my letters, but it turned out really well. I recommend 1) emailing your professors with your name, semester you took them, and your GPA in that class and scheduling an in-person appointment and 2) bringing any application materials (like a statement of purpose) that may help the professor in writing you a strong letter. The worst thing that can happen is the professor declining to write a letter, and in that case, you would have the backup of asking someone who knows you better and is more likely to say yes to writing a letter.


text:
Is it okay to mention family background in SOP?
I'm applying for MS in Mathematics. My grandfather was Math professor and my uncle is also Math professor. Such family background was one of my reasons to  study Mathematics and I was wondering if I can mention my family background briefly at introduction in SOP?

Can you? Sure, it's not wildly inappropriate.
Do I recommend it? No! This is a 1-2 page document where you state what your purpose is (hence the name). It's not a time to talk about your childhood, why you were inspired to study math, or what your favorite type of helicopter is. It's where you talk about what you've done so far and what you want to do next.
You may have to talk about your personal situation -- usually to explain a bad semester, etc. And it's fine to state a few interesting details about yourself (especially if you have significant achievements outside of math, or a non-traditional background, etc.). But listing the professions of your family members is neither necessary nor interesting.

"...or what your favorite type of helicopter is." seems unnecessary. The OP is talking about dear family members, not helicopters.

Agree it is a bit of an exaggeration ("reductio ad absurdum"), but I don't think it's disrespectful.

Could you explain more about "talk about your personal situation"? I do have a bad semseter and I want to know how I can explain such matters in SOP. Thanks

Anything that's relevant or interesting is fine. You can introduce yourself, state your hobbies/achievements, explain anything that you did that was especially noteworthy, give any mitigating factors for bad semesters/test scores, etc. Anything that you would feel comfortable saying face-to-face to your boss is fine. This is just not the time for "therapy", childhood issues, or boring stories. If you would cringe saying it to your boss's face, don't say it in your essay. (Your motivation to study math isn't cringe-worthy, but it's not something your boss would probably be interested in)


text:
Seriously conflicted about a graduate program option
I graduated in 2013 with a degree in Botany from a state college on the west coast. Since then, I've worked for the Forest Service on a rare plants/ invasive weeds survey crew, and currently, work for the USDA as part of the Agricultural research service as a biological science technician. When I took the job, I was clear to my supervisor that I planned on attending graduate school after the two years I was committed to on the project. He was excited about this and very supportive of me. I went to work for on a number of projects involving plant physiology, plant biology, remote sensing etc. My goal with this position was
to take my academic record from my times as an undergraduate and supplement it with some applied experience, then to apply to graduate schools for the 2016/17 school year as a top tier candidate. I've worked hard to make sure my undergraduate grades, GREs, and letters of recommendation are of sufficient quality to single me out from a crowd of well qualified applicants. My thought was that this two years of experience would take me over the top, that this experience would take me from being a well qualified applicant to a top tier applicant/ the top applicant. I had been looking at applying to 3-4 top tier schools in plant genetics/ plant physiology (UC Davis, UC Berkeley, Cornell, Michigan State).
So fast forward a year and a half (this summer) and my boss approaches me with an offer. He wants to fund me to do a graduate program at the local land grant university. It would be a full assistantship and tuition waiver for the two years, which is an incredible offer. I wouldn't even have to apply to the school.
Here is my conflict: The offer is for a program I'm only tangentially interested in (weeds biology), from a department I don't really want to be involved with (crop science; but could make do), at a fairly low ranked state university.
I also feel like I've set myself up for one good shot at getting into a highly competitive program, and that taking this offer will throw that away. I won't get the chance to use the letters of recommendation, undergraduate grades, GREs, that I worked hard for, only to go to a middling school to do a degree that I'm only kind-of interested in.
At the same time, it's a convincingly good offer, one that I would be incredibly unlikely to get again.
Note also, that the offer was made at a very strategic time. The offer would be for the 2015/16 school year (I wouldn't finish my 2 years under my original contract). He made the offer in such a way that it preempts my ability to apply to other schools and cultivate a counter offer.

If you don't want to do it, then don't do it. Politely decline.

I'm not sure about the plant genetics field specifically, but several of those top tier schools will waive tuition and give you a stipend. I'm most familiar with Cornell's program, but last I heard a research assistantship at Cornell is much larger than at smaller schools. So I don't think worrying about tuition/stipend should be a large factor in making your decision.

several of those top tier schools will waive tuition and give you a stipend — This is not only true of top-tier schools.  If they accept you but don't waive your tuition and pay you a stipend, they don't really want you; go somewhere else.

I don't understand "He made the offer in such a way that it preempts my ability to apply to other schools and cultivate a counter offer."  How does one do that?

I'm unclear why you are considering the offer, if you aren't really interested in the subject, and don't like the university. Do you not think you can do better?

I'd just state that the offer, while tempting, is second selection for you, and apply to the schools that interest you anyway. Worst case, you'll be rejected elsewhere. Don't close options unless you really have to.