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How to deal with a leech student?
I've been on a couple of research projects with a few professors and have had some success recently and plan to do more collaborative work through the end of this calendar year.  One student is constantly leeching off of me and imposing himself, such as wanting specifics about my work, specifics about private meetings between me and my research advisors, wanting to come to lab while I am there to do some work. (he is not part of the lab.)  How do I tell this person to back off and do his own work, establish his own connections and stop creeping on me and stalking my every move in hopes of leapfrogging me, just because I've had some recent success?  Do I have to continually say, "this is private and ongoing research that isn't published yet"?

I imagine that the answers you will get will be more on the correctness ballpark, but from a practical standpoint, the sooner and clearer that you express it to this person, the easier you will make your life. Another question is how to stay perfectly cool with this person and achieve your goal; that is more complicated. Ask yourself what are you really looking for, this is a trade-off you have to assume

Be assertive. If they ask questions about something you prefer not to discuss, say "I do not want to discuss this." If they ask to come along, say "This is important/private business, you can't accompany me." If they come uninvited, say "You are disturbing my work, please leave." Don't try to explain, just say no. If you give them nothing, they'll stop bothering you. Obviously, doing this might have an effect on your social reputation. But it's important to keep in mind that this person is not  your friend and probably never will be your friend.

Depending on the situation, you might try to put them to good use.  For example, if you're an avid researcher but you find promoting your work and networking to be tedious affairs, you might offload them to this other student.

Is this student your peer, or are you in a more senior position? (E.g., you are a PhD student with a few years of experience and he is a master student).

How about just tell him to mind his own business? Are you afraid or what?

I have seen many similar situations, and often the student managed to grab something, coauthor-ship, collaboration etc. Be careful a learn early how to keep your work private, tell straight but polite that it is still ongoing work, not published therefore confidential. Also, you may want to learn how to tell white lies: uninformative answers to his questions, if you don't want to be too blatant.

Your time is yours to control. If someone just wants to meet to learn about your field, it's polite etiquette to give them a brief meeting and let them learn... it is a learning environment, after all. It sounds like your situation has progressed well beyond that. I would simply tell the student that due to your own time constraints you cannot continue meeting with him. Consider redirecting him to the department chair/administrators, where he can ask about the process for joining a lab.
For what it's worth, if it's really beyond academic interest and he's just a stalker, that changes things a bit. Definitely work with whatever resources  your university makes available to figure out how to deal with a stalker.

You seem to assume the worst case scenario. The student may be genuinely admiring you. It is common in the industry to shadow someone for training purposes and the person may be assuming it is ok here as well. Also, some people are bad at picking cues, so he may be oblivious to your discomfort. Or even worse - painfully aware, but feeling he deserves such a treatment because of his lowly status.
Now, you of course have every right to not wish to mentor this person in any way. So I would suggest to be open but also generous with him. At the end of the day, you may need his help later, so it won't hurt to be nice now.
More practically:

Select a time to address this issue in private in a separate meeting. For example, invite to have a lunch or coffee together.
Summarize the problem in neutral terms
Acknowledge his good intentions (even if you believe otherwise). Sth like "I appreciate you want to learn how to be a good researcher and it is flattering that you think I am one".
Give an objective (preferably external) reason that has nothing to do with him personally. For example, by letting him into the lab/sharing details of private meetings you are violating a policy and can face repercussions. Or your supervisor doesn't appreciate external people in the lab or meetings. Or, as much as you enjoy his company, you really can only focus when you are alone. Don't invent a reason though.
Offer a practical alternative. "I actually think you will learn most by doing A, B, C rather than shadowing". A, B, C can be a book that you read at some point that really illuminated you. Or some best case practice of being a good researcher. Or perhaps you don't mind having a monthly "mentoring" meetings with him. Maybe  he has a specific weakness or an under-leveraged strength, and you can advise on to how to work on those. Whatever lifehack you feel comfortable sharing and that can genuinely help the other person.

This is a companion answer to the one written by @olgak.  First, quoting Olga:

The student may be genuinely admiring you. It is common in industry to shadow someone for training purposes, and the person may be assuming it is ok here as well. Also, some people are bad at picking cues, so he may be oblivious to your discomfort. Or even worse - painfully aware, but feeling he deserves such a treatment because of his lowly status.

This is very insightful.  But where I differ from Olga's suggestions is that to my mind, she's neglecting to consider the role your advisor or P.I. can play in addressing the problem.  So here's my slightly different answer:

You can, optionally, try, once, to get some more distance with this eager beaver, hopefully without bringing offense (the flavor of Olga's suggestions is great for this).
If that doesn't work, or if you don't want to play that role, let your primary advising or collaborating professor know that you are uncomfortable.  Don't make it sound like a complaint yet (reserve that for the future, if this first step doesn't work), and try to give the eager beaver the benefit of the doubt in your description.  Your main message needs to be be

(explicitly) In his/her eagerness, J. Student has been asking me lots of questions about my research, and I'm uncomfortable and unsure how to handle it.
(implicitly, i.e. I doubt you'll need to say this out loud) Can you handle this for me, please?


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How do schools determine their curricula?
What is the process that gets a textbook into the course schedule? To what extent is the degree program considered, rather than just the individual course? What part does each party play, from administration to professor to publisher/author? Further, how is it done for alternative media such as videos or video courses and software?

A bit of context: I have a business that sells videos of CME conferences and would like to explore how I may provide access to that content to the students (and faculty), whether part of a curriculum or not. With this in mind, I'm looking where my business might fit in and make a deal with a school.
For example, I'd be happy to offer access to individual lectures to augment a course, entire courses to augment a program, or just exposure that might convince students to purchase the videos for their own interest (e.g. a link on their website, a place in the book store, email list, professor's "extra reading", etc.)

To clarify, by "school" here you mean a university?  Primary and secondary schools have very different processes, and are outside the scope of this site.

@Nate Yes, I mean post-secondary institutions. College, university, grad-school, etc.

(This applies to US universities; not sure if the rest of the world is similar.)
Textbook decisions are, by default, made by the individual professor teaching the course, based on what they feel is most suitable for the course.  They would of course consider how the course fits into the degree program(s) that require it, but there usually isn't a concerted effort to have consistent textbooks across all courses in a degree program.
For "standard" courses that are taught regularly by many different professors, the department may choose to adopt a standard textbook.  This decision would typically be made at the department level, led by the professors who teach the course most frequently, with input from others in the department, other departments whose students often take the course, etc.  For courses in which a particular piece of software is central, the choice of software might be similarly standardized.
Higher administration usually has little or no direct role in such decisions.
Supplemental materials (additional software tools, videos, extra reading, etc) are usually selected by individual professors, and are not usually "standardized" like the main textbook can be.
Bookstores will by default stock all books and other materials that are listed as "required" or "optional" for the course.  Everything beyond that is at the discretion of the bookstore manager, based on whether they feel it makes business sense.

So for my specific context, I'd need to talk to professors.

@fredsbend: Yes.  Be advised that professors get lots of advertising materials for textbooks, etc, and usually throw most of it away without reading.  I certainly do.

I'm not really interested in being a marketing research subject for you - but I pretty much ignore all unsolicited advertising for instructional materials, regardless of its content.  Recommendations from trusted colleagues are a much more important source for me.

Sorry, the question was more or less "how do you decide then", which you answered. I guess I imagine professors eventually favor certain publishers and authors, so they look for those first. Is that true?

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How soon to send dissertation to committee before defense?
Basically, I set my defense for 3 weeks from now but forgot that I will need to send my dissertation to the committee before the actual defense (it's been a busy week), and I need as much time to work on it as possible. I'm thinking I will send it to them a few days before the defense (e.g., over the weekend if the defense is in the middle of the following week). Knowing them, it would probably be fine anyway, but would that be really bad form? Just trying to get an idea of what is typical.

The exact requirements vary by institution and program (e.g., some may require a dissertation draft to be submitted to a committee within a minimum amount of time before the defense, perhaps around a week or 10 days) though I suspect that these requirements are rarely enforced. The presumption is that you will give your committee members sufficient time to read your manuscript before you present it to them, both so they're familiar with your work, and so they can catch any obvious problems with the document. It's not their job, of course, to proofread your work or even to review the entire document in great detail before the defense, but they should have the option to read it, and you may find their suggestions are more helpful if you give them more time to review. Otherwise, you may find yourself referring to portions of the written dissertation during your defense despite having only made the material available for a few days. The material is less likely to be surprising if you give your committee ample time to see it beforehand.
So, if your question is "am I good?" then your answer is "possibly, but don't make peoples' lives harder than they already are." A defense is not a good time to irritate your committee members. Give them a week, at least.

One other factor that should be considered is the academic calendar. One week might be ample time during a slow part of the semester, but students may want to add even more time if the dissertation is being handed over at an especially busy time in the semester (such as finals week).

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What masters degrees can I apply for with an undergraduate in Computer Science?
I'm a Computer Science student in the UK who is about to go into my last year and I'm looking into applying for a masters programme and I'm not sure what subject areas I can apply for. I've heard that doing a Masters in Computer Science after doing your undergraduate degree in Computer Science is essentially useless. I'm on track to hopefully graduate with a first if that effects what I can do after I graduate. I was particularly interested in pursuing something maths related.

What is your long term career objective?

I'd ideally like to work as a software engineer doing some advanced programming liek systems programming or something else in a lower level language. Or possibly something that also involves some mathematics as that would be really interesting.

Are you sure another master's degree right now is the best path? Maybe you should be looking at getting programming experience.

A masters is very different from an undergraduate degree. Perhaps discuss those differences with a member of staff.

Perhaps you would enjoy applied math.

There are many kinds of masters program you can apply for with a degree in CS, ranging from more "technical", specialized programs to non-technical ones like an MBA. Restricting the possibilities to more technical master's programs "that involves some maths" and/or advanced programming still cover a large number of potential programs, especially if you're willing to go abroad. Examples include master's in machine learning, bioinformatics, financial engineering, embedded systems, information security, data science, and scientific computing.
It'll be best if you first consider clearly which specific area you want to specialize in. If you are still uncertain about this part, it'll be good to work for a few years first. Working also serve as a kind of reality check -- you may think that you will enjoy a specialization based on your experience with a related module during your undergraduate years, but later discover that you don't really like the job scope of a typical professional in that field, or any of the potential employers in your location, or the overall long-term prospect of that particular field. In that case you can still adjust your plans before investing more time, money and effort to get a Master's in that particular specialization.


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Six months have passed since paper has been accepted and it was not yet published - has the editor changed his mind?
About 10 months ago, I submitted one little article to a journal and six months ago I received the acceptance. I uploaded the latex file and since then I didn't hear anything about it being published.
Today it appeared a new issue of the journal so I must wait at least another 3 months.
This will be my first published article and I started to become a little nervous about it.
Can you tell me if something happened, like editor's changing his mind or delaying because they consider it less valuable than other submissions?
Should I contact my editor about this?

@henning: That only aspect that Q&A answers is whether the editor may have unaccepted the paper. I would not consider it a duplicate.

Did you check whether the journal usually publishes other articles online before they are published in print? What about other articles that were accepted around the same times as yours? Are they already published?

It is very unlikely that the article has been "unaccepted", and as far as I know, most journals publish articles basically in order (modulo some special issues and things like that).
However most journals have backlogs, and can take a long time from submission of the final copy to getting the article to print.  I don't know how common that is in your field, but for math, in 2015, the AMS published some data on how long it takes math journals to publish an article; a quick glance shows that gaps of much longer than six months between acceptance and publication are common.

Many journals can take several months between when they tell authors the paper is accepted, and when the article appears in the print copy of the journal.  (This is totally anecdotal, but in my experience, the time gap between acceptance and printing tends to be larger for journals that have shorter turnaround times for review and acceptance.)
Suggest first pulsing your coauthors, peers, and/or colleagues on what their experience has been with this particular journal.  If they suggest that this is out-of-normal for this journal, you might try contacting the editor who sent you the acceptance notification.

In fact, some journals even print on the first page of each article: submission date and acceptance date.


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Where do math grads, who don't code, land up in industry?
Do they go into investment banking? Consulting? Start their own bar and restaurants? Are there any statistics known about what percentage of industry jobs for people with math degrees require coding? About what types of jobs don't require coding?
math grads = math undergrads, masters, PhDs who don't write code and have no desire to join the data science craze.

Comments are not for extended discussion; this conversation has been moved to chat.

Great question!!!!


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Is it appropriate to use emoji or similar icons in a paper?
I'm not in academia anymore, but spend quite a bit of my time reading papers and using the findings as part of my job.
Today I picked up a paper that contained a couple of emoji-type icons in the figures. It was to show which of two conditions was preferred. There's a smiley face next to the desired condition and a sad face next to the undesired one. It's an electrical-engineering/computer-science paper.
It's the first time I remember seeing something like this in a paper and it made me question the quality of what I was reading. I googled a bit and it was presented at an FPGA conference in February this year and is associated with a well-known university in the USA, so it seems reputable.
Perhaps I'm just behind the times. Is this more common than I realise?

Such things will probably have no meaning in 30 years. You are writing for the ages, not the kiddies.

@Buffy: It is hard to imagine that :) and :( will not be understood in 30 years. If yes, then probably many words we use now will also not be understood. Moreover, I think it's not appropriate to call the people using smilies "kiddies".

@user111388, I know fewer than five emojis even now. How many do you know? And if you intentionally dumb down your writing then you are, indeed writing for the kiddies.

@user111388, back in the 1960's we used lots of really cool phrases.. We were bitchin', man, bitchin'. Most people today would consider it trite and disruptive if we'd put it into papers of the time. Some of you probably need to google it to understand what I'm sayin', man.

Frankly, I think this should be done more often. It can be frustrating to read a paper with lots of scales where in some more is good (or less negative, or small fractions, etc.) Because they're pictures, they're pretty easy to comprehend

@Buffy: From the text, I understand that they talk about ":)" and ":(" and they complement the text, not replace it. Probably they are better understood than English language itself.

I'll answer from the perspective of a different field. In the biomedical sciences, it isn't uncommon to use some cartoonish representations to depict animal tasks/procedures, particularly because actual pictures of animal subjects are often avoided for a number of reasons. The same can be true for human subjects.
I wouldn't think twice about seeing a smiling versus frowning monkey indicating task performance in a figure, as long as it was instructive/guiding and not interrupting/distracting. Same for other types of icons like thumbs up/down. Certainly emojis in text would be totally different.

In my humble opinion, the use of emojis within the texts is strongly discouraged, particularly in a journal paper.
In regards to the figures, I have seen some papers that consider some, maybe funny, images to depict the senses. For example, the users of a system might be angry with the results of one approach and might be happy with the results of another approach.
As the goal of any figure is to describe a subject more clearly, the use of emojis in the figures of a paper is acceptable, and sometimes it may even help the readers better understand the problem.

If I remember correctly, Craig Smorynski once (or maybe more than once) used a smile symbol for "end of proof" and a frown for "end of counterexample". I think this is OK, but when I (only once) tried to do the same, the editor didn't allow it.

Could you say for context that reader don't have to look it up who Craig Skorynski is? Is he famous in his field?

@user111388 Craig Smorynski is a mathematical logician, the author of several books and of a proof theory chapter in the Handbook of Mathematical Logic.

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How to leave a PhD without angering my academic references?
I opted for a PhD at the same university where I did a two years master’s (I'm an international student). The master’s level was remarkable, but the PhD isn't that good. It feels like an extended version of the same master's. Since I’m not receiving the training I expected or being exposed to the challenging problems that could put me at the forefront of my field, I have certainty I must leave this PhD for the well-being of my career. I have talked to the students' counselor, voiced my concern about the prospect of my training to my direct supervisor, asked authorization to reshape my project (no professor has experience in the theoretical direction I want to take it) or to go abroad as visiting student in another institution (my funding is very strict in terms of leaving for extended periods) and reached the conclusion that the possibilities of improvement are slim. Nonetheless, I have tried to keep the tension low and not sound menacing ("either you let me do this or I'm out").
I’ve identified other PhDs (or even jobs) in which I could achieve goals more in line with my expectations. But there is a problem. All my relevant academic network was built during the masters and is therefore in the same department I’m planning to abandon. Although they've addressed my concerns in an attentive manner and encouraged me to continue, I'm sure they won’t be happy to let me go and some may even take my decision as an insult to the department and a PhD program the university is very proud of. But I heavily depend on them too. I’ll need their letters of recommendation to apply to graduate school elsewhere or get a job. Has anyone secured a letter of recommendation from a supervisor you parted midway your PhD? How to voice this type of decisions in a non-confrontational way? How to deflect the conflict and leave the PhD without shooting myself on the foot?
Full-disclaimer: I’m not angry, lonely, depressed, burned-out, in debt, amid a fight with faculty, etc. I’m just dissatisfied with the quality of my PhD, which, true be told, could be very good for other students; it’s just that I already got this training during my master’s!

I'm not saying you shouldn't quit. But have you shared these frustrations/concerns with your advisor(s)? They may not even be aware of your frustration -- and if they were, they might be able to help you find a new topic/research direction.

What year are you? At you school, where does that put you in the program - Are you still taking classes? Are you involved in research with faculty? Have you defended a prospectus?

@tonysdg I have voiced that I wanted to change the focus of my project into a direction I think is more promising and got authorization to do it. The problem is that no professor has strong experience in that area and I would be almost self training myself the next year or two. This is a relatively small department and choices are limited.

@Dawn I'm eight months into it. I finished classes and am in the early stages of the research process.

So the faculty have responded to your request for a more interesting problem. You are at a position in your graduate school development arc where you must take more personal responsibility to execute your project. You don't want to do the 'self training' that is required to develop further as a researcher. Why will it be different somewhere else?

@JonCuster I'm totally aware that a PhD student is expected to be a highly independent learner, but total lack of mentorship is also a recipe to PhD failure, and that is essentially the position I was put when asked to reshape my project.

Fair enough. So, is there a chance to work through your advisors to connect to other people at other places to collaborate with? This could even involve you spending time at the other institution, broadening your horizons. Still, before jumping, you should evaluate deeper what is bothering you or else you risk it happening again. Many people dread the leap from being a student taking courses (like you have been doing for years) to the seemingly empty void of research.

@JonCuster There is chance for collaboration, but more of a short visit than a real internship (It has to do with being an international student... This is disappoint fact about the PhD I wasn't told about until I started inquiring).

Just because no professor has experience in the direction of your interest, that doesn't mean you can't pursue your direction of research at your current site.  If you don't see a path forward, it means that you've been unable to establish a plan to do so.  Many profs would be pleased to have you as a resource that will help them expand in new and exciting directions.

Reading more of your comment trail, you haven't said anything to lead me to believe that you would have a "total lack of mentorship".  Yes, you might be driving a bunch of research on your own, but you would most likely be guided by a very competent mentor,  though maybe not perfectly versed in the exct area you're interested in.  If you don't want to piss off your department, not using hyperbolic language would be a fine start.

Along the same lines as what @ScottSeidman and JonCuster are saying, note that the student-advisor relationship isn't necessarily limited to deep content knowledge in the area you are studying. If you have support in analyzing/editing your writing, funding/finding funding, navigating conferences and networking, navigating departmental politics, and understanding the requirements and expectations for your degree from your program, those are all types of mentorship that "count." If your subject knowledge passes your advisor's, but you have an opportunity to teach them, that's still mentorship.

You'll need to be a minimalist in your communications, and stick to a consistent line: you wish to change programs to seek a better fit.  Better fit.  Better fit.  No more, no less.  Practice until you can say it in your sleep.  Better fit.

Note that I have exhausted all the logical possibilities

It doesn't sound like you have, though. You need to explain, in very clear terms, that you are unhappy enough to leave the program and apply somewhere else.*
Don't hold back, but I would avoid using vulgar language (you know, like in your titular question), and would otherwise strive to be professional about it.
Now, most academics are sane, understanding people. If your advisor comes up with some potential solutions that, after reflecting on them, you decide are not satisfactory, then you should make your decision to leave the program and ask your advisor for a strong letter of recommendation. (I would encourage you to be patient when working through the potential solutions with your advisor, though, as there may need to be some iteration.)
The key here is to really, really, really make every attempt to find some common ground with your advisor that works for both parties before deciding to "jump ship." I don't see how a sane, understanding advisor could possibly hold against you wanting to put yourself in a better situation, so long as you make every possible attempt to make things work out where you currently are first.

* I don't mean to be rude, but from the comments below your question, you seem to have an answer for everything, so I want to minimize that type of interaction here. My impression is that you are beating around the bush with your advisor, and not really giving them the "full scoop." Just basically tell them what you have told us here, but in a professional manner.


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Should I take a student loan now, if I intend to become a mathematician?
I intend to pursue my degree in Mathematics and Physics at Ecole Polytechnique in France. The institution has offered me an interest free loan of 18,000 euros, which has to be repaid three years after I complete my bachelor's degree.
Since I am passionate about basic sciences, I hope to join a five year PhD programme after my degree and this usually comes with a decent scholarship/stipend. Approximate salary for PhD scholars in Europe is about 1300 euros, though this might vary from institution. Right now, I am not sure whether this salary and the one received during Post-Doc might be enough for me to repay these loans and therefore, I wish seek advice on this matter from the Academia Stack Exchange community which, I believe, will be in a better position to answer  this question since most members are pursuing a career in Academia.

If you graduate at École Polytechnique, you will be coming out with a Masters on top of the Bachelors degree. Are you sure that the date is 3 years after you obtain the BSc instead of 3 years after your graduation? By the way, check out the Paris Saclay and Jacques Hadamard Foundations scholarships for international students.

I'm not sure how postdoc salaries fit in here, since it sounds like the loan will be due before you finish your PhD.  Whether you can repay it out of your PhD salary would of course depend on how much money you spend on everything else (which in turn depends on the cost of living where you study, etc).  So it's hard to answer for sure but in any case it sounds like it would be very difficult.  Is there any possibility of refinancing the loan after three years?

Have you checked with the Ecole Polytechnique if repayment for this loan would be deferred for people in graduate studies?

I would probably focus on completing your undergrad first. It's great that you have a life plan, but it may be that you change your mind about wanting to pursue a research degree/academic career afterwards.

Just one question: do you need it?

@MarkoKarbevski Ecole Polytechnique has recently started a Bachelor's program, which is different from the Ingenieur Diploma program and thus I will not lead to a Master's degree after graduation. Details about the program can be found at this link (https://portail.polytechnique.edu/bachelor/en).

@NateEldredge I am not aware of any possibility of refinancing the loan, since all the documents pertaining to the loan have not been sent to me. The program coordinator has only outlined the basic information. Beginning from my first year as an undergrad till the end of the 6th year, I do not have to pay anything. Repayment starts from 7th year and must end in the 10th year. I would thus have to 4500 euros per year.

@AlexanderWoo Ecole Polytechnique expects that after my 3 year bachelor program, I will study for an additional three years. Therefore, the loan repayment starts in the 7th year.

@MikeMiller Certainly that could be the case. But I have to make a decision now and I don't want to regret this choice later on.

@Greg It will be hard for my family to afford the education otherwise, but if we stretch our finances then I probably won't need the loan.

I'm voting to close this question as off-topic because it is more about personal finances than academia.  It might be on topic at Money.SE

@Supermario: Ah, I misunderstood - I thought you meant you had to finish repaying the loan by three years after your bachelor's.  If this gets reopened, or reposted somewhere else, please clarify that in the question.  Also, by "refinance" I meant taking out a new loan to pay off the original one - so it wouldn't be described in the loan documents, it's more about what other loans might be available in your country.

Please do not vandalize your posts.

@ΈρικΚωνσταντόπουλος How do I remove it, I mean the question?

@Supermario 1) closed questions aren't necessarily delete-worthy 2) you have already got an answer to this question, and the answer is high-quality and not yours 3) when you joined this site, you agreed to terms that specify that, after you post any content, "You grant Stack Exchange the perpetual and irrevocable right and license to use, copy, cache, publish, display, distribute, modify, create derivative works and store such Subscriber Content and to allow others to do so." (section 3 in legal)

Before answering whether you should take the loan you need to ask yourself some basic questions.

Would I go to the school if there was no loan available?
How would I pay for the school without the loan?
Are you good at budgeting your money?

If you would not go to the school without the loan, the answer to the big question depends on why the loan influence's your decision. The answer is almost always that debt is bad. If you would go to the school without the loan, have a means of paying for school and are good at budgeting, then take the loan and put it in a secure investment. At the end of the 3 years, cash out the investment, pay off the loan and pocket the interest. If you are bad at budgeting, you want to be careful about taking on debt and the answer is almost always debt is bad.

Thank you for your answer! I don't think that it would be possible for me to attend this program without the loan unless my parents really stretch their pockets. The fact that the loan is interest free is what makes it a bit compelling for me to consider attending this college. Plus it has a great math program too.


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Is a Harvard PhD in applied mathematics (from engr. dept.) as reputable as a PhD in pure mathematics (from math dept)?
Most rankings systems rank math at Harvard quite favorably. Is phd in applied mathematics (control theory) at Harvard as reputable as a phd in pure math at Harvard? (The first is offered in an engineering department while the second is offered in a math department)

Surely not to pure mathematicians.  Why don't you look at specialized rankings for applied math?

I don't see how pure mathematicians would have any say in this issue.

If you pay for the US News graduate school rankings, is there a ranking for "Applied Math"? I didn't pay, so I don't know.

@GEdgar: there's a lot of information you can get from US News graduate school rankings without paying. "Applied Math" is a subcategory of "Mathematics", and Harvard doesn't even make the top 14 (despite being in the top 4 for math).

lol, it is even harder to get in Harvard through applied math because only one or two students are taken each year.

I got my PhD at Harvard in mathematics.  Not in "pure math" but just in "math."  Harvard does not have an "applied mathematics" department or a "PhD program in applied mathematics."  Rather, applied mathematics is one of seven "areas of study" in the school of engineering and applied sciences: see here.  What does this mean?  Well, see here.  It says:

In keeping with the interdisciplinary nature of modern research, we do not have traditional academic departments and do not award degrees by specific research area. Instead, graduate students work toward a degree in one of seven subjects—Applied Mathematics, Applied Physics, Computer Science, Computational Science & Engineering, Data Science, Design Engineering, and Engineering Sciences.

Some of these subjects have "PhD model programs," but when you click on applied math, you find

Due to its highly interdisciplinary nature, Applied Mathematics does not have a specific model program.  Students pursuing a Ph.D. in Applied Mathematics should consult with their Director of Graduate Studies: Professor Ariel Amir (fall), or Professor Yue Lue (spring), concerning their degree programs.

Interestingly, Professor Amir is an Assistant Professor of Applied Mathematics.  [Interesting in part because the mathematics department has had only "full" professors for at least 20 years.]  Here is a listing of faculty in applied mathematics at Harvard: the only other professor who is listed as being solely in applied mathematics is also an assistant professor.  This suggests to me that applied math at Harvard may be in the process of becoming more of an academic department than it has been or is now.  The time would be ripe, in view of the record $400 million gift of Mr. Paulson in 2015.
All that was mostly background.  Now I can tell you: when I was at Harvard (1998-2003) there was almost no direct contact between the mathematics department and the mathematics part of SEAS: I knew one SEAS PhD student who was (for some reason) teaching freshman calculus along with the math students.  (I just looked him up: he has what looks like a lucrative industry job in Boston.)  So the answer to your question is: No one I know is comparing these two programs. They are different in every way, with almost no overlap.  It's not as though you could choose to do control theory in the math department at Harvard: there is no one there that does that.  (There is one professor in the Harvard math department who does what I at least would call applied mathematics: Martin Nowak, the Professor of Biology and Mathematics and Director of the Program for Evolutionary Dynamics.)
It would make more sense to compare the engineering program at Harvard to other engineering programs.  US News ranks Harvard's engineering program at #23 currently.  If you look at this page it gives you the ranking of a variety of programs at Harvard, and actually it has the lowest rank of the more than 100 programs and subprograms listed there.  The math department is currently ranked third [it has been ranked in the top three for many years].  So maybe that is a sense in which "pure math is more reputable," although again I stress that this does not seem like the right way to look at it.

It seems to me you're saying that Harvard Math and Harvard Applied Math are like apples and oranges. The comparison between them doesn't make too much sense. Is my interpretation very much off?

@scaaahu: That's exactly right.  I even thought of using such a phrase -- maybe I should.

Nowak, not Novak.

Despite their idiosyncratic refusal to divide SEAS into departments, you can still classify the faculty into Applied Math, Applied Physics, Computer Science, and various flavors of Engineering. They aren't one big interdisciplinary research institute.

While Pete's answer is correct in some sense, I think there's another important one.  To most people in the world, they will just hear "Harvard," "math" and "Ph.D." and think you're a genius; from the perspective of these people, these might as well be the same.  So, if your goal is to impress people who aren't experts, the difference between the programs is basically zero.
If your goal is to be successful in academics, then the overall reputation of the program is somewhat secondary; people won't care how venerable the program is if you can't show something significant you personally did.  The overall program is only important because of the networks it gives you access to (both of students and professors) and to some lesser degree the classes you have an opportunity to take.  That's maybe a slight exaggeration; having a name like "Harvard" on your degree will probably help you get people to look a little more seriously at you, but it won't do you any good if they don't like what they see.  Again, from that perspective, either program will probably serve equally well.

If your goal is to impress people who aren't experts, getting a PhD is an inefficient and quixotic way to attempt this.

Applied mathematicians themselves know exactly how good other applied math programs are. If you want to advance in academia, you need to impress other applied mathematicians. Going to an inferior Applied Math program at a very good school isn't going to fool anybody who really counts. (This is not to say Harvard has an inferior Applied Math program ... even if they're not in the top tier, they're still very good.)


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How do the grades of higher degrees equate with undergraduate qualifications, in terms of quality of work?
How do the grades of higher degrees math up with undergraduate qualifications, in terms of quality of work? I'm in the UK. At my current institution, where I'm sitting an MA

70+ -- Distinction
60+ -- Merit
50+ -- Pass
< 50 -- Fail

At undergraduate, again in the UK

70 -- 1st
60+ -- 2.i
50+ -- 2.ii
40+ -- Pass

I would very much like to know if the standard of work matches up to the same percentiles, in the UK. So, not how well someone is doing on the course, but if an undergraduate dissertation could be handed in and get the same mark on a Masters. This seems unlikely, of course.

I'm not familiar with the UK system, but in the US it's common that graduate grades are interpreted very differently than undergraduate grades.This is because the objectives and constraints of graduate education are very different than undergraduate education, so I'm guessing the same is true of graduate student grading the world over.

got it. but there is a sense in which any work can be compared according to its very own quality... high school vs university? -- surely ... @David

I'm not sure what you're asking.

"Standard of work" is a rather vague term in my opinion. I would obviously expect the standard of work for a graduate student to be significantly higher than that of a high school student. But within any individual age group, defining a standard of work is a relative matter. Some students will likely perform better than others, some will likely perform worse, and others will fall in-between. If you're asking about a way of objectively defining that standard -- then no, I doubt you'll ever find such a thing.

...additionally, if you're asking whether or not you can compare a "high standard of work" for a high school student to a "high standard of work" for a graduate student -- again, the answer is probably "how would you even compare their work in the first place? One's answering questions in a textbook, the other is writing the textbook."

@tonysdg i get what you mean, but i don't think you unequivocally cannot compare the standard of work in different settings. how do you compare good science with good math?

@user3293056: Personally, I don't, and if I'm being honest, I also can't. Part of that stems from the fact that most individuals (like myself) don't know enough of both topics (or any two topics) to be able to make a straight comparision between the two. But you chose an excellent example -- math and science. I'm a computer engineer; I have a good friend who's a mathematician (or mathemagician, if you ask me). He hates the simplifications I make in my calculations; I can't stand the precision he insists on. Yet each of us (I hope) does a "good" job. It's just relative to our field.

You state (emphasis mine):

"I would very much like to know if the standard of work matches up to the same percentiles, in the UK. So, not how well someone is doing on the course, but if an undergraduate dissertation could be handed in and get
  the same mark on a Masters."

If this were possible surely the need for Master's degrees would not exist. Besides, don't you feel that the standard of your own work at Master's level is much higher than that at undergrad? I know mine certainly was. That's kind of the point.
Say you need to get a 65 at undergrad to start a Master's degree, but you end up failing the course and getting zero. This doesn't nullify the 65 you already achieved in your undergraduate degree- but nor does it mean that you should have also got 65 in the Master's course.
The root of this answer is that you simply can't compare apples and oranges. Undergraduate and Master's degrees are designed to do completely different things, and just because one piece of work satisfies the requirements for an undergraduate degree does not mean it will satisfy the requirements for a Master's (and vice versa).

Of course, and while probably statistically accurate, this type of answer presumes a certain passivity (and non-precociousness) on the part of students at all levels. Yes, such assumptions are nearly universal on the part of academic institutions, and may be statistically accurate, so to respond in this fashion is completely reasonable. Nevertheless, in principle, the question could make sense. That is, an exceptional undergrad thesis could also be an exceptional M.S. thesis. Or even an exceptional PhD thesis. [cont'd]

[cont'd] Although I'm in the U.S. and our way of appraising theses at all levels does not attempt to do so in terms of "percentages" or "comparisons" to cohorts, so maybe I completely fail to understand the U.K. context, still, surely not all appraisals of theses are based on the "curve" of comparison to one's cohort. E.g., if a reasonably good person by mischance is compared to a gang of exceptional people, they have no chance of passing? Such things.

@paulgarrett The UK system does not evaluate students based on the entire cohort. Rather, in theory, theses should be evaluated on an individual basis. That is, a reasonably good thesis should receive a resonably good mark, even if compared to exceptional theses. Though in practice, it is not easy to stay completely objective when assessing theses of vastly different quality.

@paulgarrett re: your first comment, I agree in principle with what you're saying, but in reality, what undergraduate thesis has the depth, originality and maturity of writing to be comparable with a PhD? My logic when writing this answer ran thus: a Master's is inherently more valuable than a bachelors, therefore a bachelors is inherently less valuable than a Master's, hence while a numerical grade may be the same in both, the value of that grade differs depending on the qualification it is part of. (1/2)

(2/2) Thus, the answer to the original question ("How do the grades of higher degrees equate with undergraduate qualifications, in terms of quality of work?") is that you simply cannot equate them. The quality of work done is significantly different (except in the case of some hypothetical super genius who wrote an undergrad dissertation so good they were automatically awarded a PhD).

Yes, again, it is unusual that an undergrad thesis might be comparable to a PhD thesis, but it's not that there's a rule or convention that makes it be so. And, in the U.S., it's not that a super undergrad thesis automatically gets a PhD, although it may make that path easier. Yes, statistically there's no point in attempting (and mostly failing) to compare one level's thesis with another, but that's not because of any intrinsic reason, much less some conventions about percentages and grades.

@paulgarrett I'm finding your last sentence quite difficult to parse (but we should probably move to chat if we want to talk further). Either way, I would be interested to see your own answer to the question. I am wondering if I misunderstood it.

To better respond, in effect, to @astronat's responses to my comments on their own answer, and also to clarify my reaction to the original question:
First, I cannot endorse any notion that scholarship, research, and advance of our collective understanding(s) are measured by "grades", scalar numerical values, hono(u)rs-or-not, and so on. Nor can I endorse the idea, implicit in much of academe, that students and teachers are somehow antagonists, in the sense that students are (allegedly) trying to avoid education, or that teachers should be trying to "trick" students by bait-and-switch in order to make them fail to some degree... supposedly for their own good.
Also, of course, any given individual mostly does better at everything when they are older, thus having acquired more information, and having matured. So any given person's undergrad work is presumably less sophisticated than their post-undergrad work, and so on.
Nevertheless, I think is it profoundly misguided to think that the institution(s) have any sort of true measure of students' progress, nor of their "success". True, there is the obvious general correlation of age and maturity/sophistication, but this is not due to any rules or conventions. So, again, undergrad work tends to be more naive than later work. But this is not a rule, and is not a property of universities and their administration.
So, although it is not really purposeful in general, yes, one could compare various peoples' work at different stages of their development. Yes, some undergrad work is as good as or better than some graduate students' work. So what? And, in particular, any pretense of giving "objective" comparisons, in terms of percentages, in whatever meaning, is not to the point, and probably unjustifiable in any sane context. If nothing else, no matter how wonderful a lunch someone else has, one still wants one's own lunch.
I think that "grades", "impact factors", and other numerical artifacts give people an over-simplified, and grossly misleading, impression of the (worthwhile) goals of scholarship and research. E.g., that it's a competition. Yes, the administrative powers can make it be a competition, and can unilaterally declare that GPA or impact factor are the scores that matter, but that does not make such things absolutely true... only contingently true, for the usual reasons.
In summary, first, the original question is a bit misguided (in my opinion), although understandable. Second, with some disclaimers, there is in principle no reason that undergrad work of exceptional people couldn't surpass that of grad students, etc. Third, no, this happens rarely, for obvious reasons. Fourth, and this might be the most immediate point here, I'd disrecommend thinking that institutional/bureaucratic fake objectifications of all these educational/research/scholarly processes truly represent reality. In the latter sense, the question itself has been corrupted into granting several implicit hypotheses that have certain appeal, if only that reality really is that straightforward, while, in fact, reality is not so simple, both for good and for ill.

Thank you, I now understand your point much better and for the most part, I agree.

@astronat, good! Thanks! A quip I use with grad students at my uni is that the notion of mathematics as "a school subject" is wildly corruptive: mathematics (as an intellectual/scholarly pursuit) is not about grades, honors, or any other similarly bureaucratically-mediated thing! In fact, grad students (in math, at least) do often become a bit confused by the notion (which I aggressively promote) that the goal is not to guess what the "teacher" will put on the final, nor to do all the homework perfectly, nor... but to do a thing which has no convenient measure. :)


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Supervisor does not allow use of commercial software for student project, against student's interests
My supervisor does not allow me to use commercial software for my project. I believe that they want to reuse, modify and build upon what I do and thus are interested only in tools/libraries that are widely-accepted in the scientific community (which I do not intend to pursue a career in).
The commercial software products license costs are not an issue as students can either officially use the software for free or licenses are quite cheap (e.g. less than 5 Euro for students). As I know which tools are used in the kind of jobs I want to get in, I do not need the supervisor "to guide my software decisions" to help me in this aspect. I am also already quite proficient in one of the commercial software tools I want to use, but I feel my supervisor is not (and also has no interest in learning more about it - I do not blame him for this).
When signing up for the project, usage of commercial software was not explicitly excluded. The topic of the project itself is actually interesting, it is just the software that we cannot agree on.
How might I persuade them to change their view? If impossible, how can I make the most of this situation?
This question is related to what I am asking about, but it is more normative in nature.

Comments are not for extended discussion; this conversation has been moved to chat.

It seems like you think that how you carry out your research should be directed by the job you want to get when you leave academia. This is not your supervisor's concern, nor the concern of the wider academic community.

I'm genuinely conflicted as to whether or not "Ethics" is the appropriate tag here - that seems a little strong.

Are you talking about using some sort of commercial software to do something "normal" (design a widget with Autodesk, Altium Designer, other CAD/EDA software), or buying into an entire proprietary framework (programming in MATLAB, LabView, SAS, ArcPy, etc.) that might be incompatible with some academic fields?

What is your topic or field of research? Is computation central or incidental to the research?

@jwg so the job prospect a student is not something a mentor should care about? That seems a little bit arrogant.

How about sucking it up and following the rules set by your teacher? You are there to learn, aren't you? A teacher have any right to specify a computational project, esp if he wants you to make a calculation that may be fully automated in some of the commercial software or otherwise interfere with the purpose of the project.

I would see it as a great opportunity to learn the free tool, and it should be easy if you are already familiar with something similar. I regret that I used matlab during my phd, when I should have learned Python & C++ (I now work in the private sector).

Consider also the problem of scaling it up. We used to use some programs in MATLAB, and even though we can get some affordable personal licenses, we cannot use them in the computer cluster, so we had to replace them for large scale applications.

The student license can be cheap, but the standard license is probably not. If the chair doesn't have funding for a standard license, or they are not interested in this specific software, the lab will end up with an unusable piece of software as soon as you leave. This is certainly not in the interest of the lab.

What would you advise me to do?

There's not much you can do: either accept the chair's choice of software or go find a project in a lab which uses your preferred choice of software.

This is the a large part of the reason software firms giving free student licenses: when the students are no longer students, if they want to keep using the software, the expensive licenses must be bought :)

@Massimo: I also just outlined this in a comment above: Viewers are available for free. My work would still be useable, but modifying it would be costly (even though I think PhD students are as well eligible to get the software for free/at reduced cost as they are also still students). Please also consider the problem from my perspective: If I follow the lab's preferred way of implementation, it is kind of me who ends up with an "unusable" piece of software, so to say. I think it would be best to come to a compromise as both parties involved spend time on the project.

@UnitRoot People do not change tools and workflow they are used to, unless you give them a strong motivation to do so, and definitely you're not giving them any motivation. If your program turns out to have a serious bug when you are no longer around, people in the lab should be able to fix it in a reasonable time, which would be impossible if you implement it in a software they're not familiar with. The fact that you end up with an "unusable" piece of software is irrelevant for the lab's chair, because they make the lab's interest.

@Massimo: I see your point and thank you for clarifying it. Still, I don't think that's an ethic I would follow. If someone was working for me without getting paid, I don't think I would require them to give up their interests to this extend. Also, my university is not "owned" by the academic staff. They so to say also get paid to engage in teaching/making sure people get educated for the sake of the economy of the nation. I always thought studying was about becoming a critical thinker and learning how to get things done on your own instead of relying on being told how to do things.

@StephenS: There are some valid reasons for using commercial software, I think: (1) Usually, training employees to use them is a lot cheaper as their UIs are more easy to use. (2) Most business users don't need to know how they could do rocket science, but how to be efficient (3) If business decisions rely on your work, management will not want your numbers/results to come from non-commercial software as they have to make sure there is someone that could potentially be held accountable for errors. Management owes this requirement to their stakeholders who might be affected adversely.

@UnitRoot your point 3 is  wrong. Software companies aren't generally accountable for errors, while for open source code there's at least the option of checking it.

@UnitRoot. You seem to be conflating "Free Software" and "non-commercial software". This is an error. Red Hat Enterprise Linux, for example, is definitely FOSS, and is definitely commercial.

@UnitRoot, Re: "training employees to use them is a lot cheaper as their UIs are more easy to use.": the gains on the ease of training are offset by the losses from future vendor-planned interface obsolescence and format lock-in.  Read the fine print of the license agreement where they absolve themselves of responsibility for whatever those cost you down the road.

@StephenS They learned valuable lessons from drug dealers.

An important consideration, is how are you going to be marked / judged / assessed? On your scientific results, or on your software contributions to a larger project? If the former, you have a justifiable complaint that you are being forced to work "with one hand tied behind your back". If the latter, or if it is pure work experience with no assessment, it's reasonable that you learn to use the established toolset, not your own first choice, and learn to be a "team player".

You are confusing your academic training, which should focus on instilling in you a good understanding of the theory, with the practical training which you will pick up through working or spending your own time learning a specific tool. While I do appreciate the need to make yourself as employable as possible, I would also say that it is important for the academic community to utilize tools that can be freely used by anyone in order to ensure that future research doesn't get locked into specific commercial toolsets.
Also depending on your area of work you may find employers these days are moving more towards open source anyway (certainly the case in data science).
My suggestion is to do the work using the tool your tutor suggested but pick one part of your project to replicate in the commercial tool. Employers understand why the academic community may not use commercial tools (as they grapple with the question of licensing costs themselves) but will be impressed by your willingness to go the extra mile to learn a tool.

 it is important for the academic community to utilize tools that can be freely used by anyone in order to ensure that future research doesn't get locked into specific commercial toolsets. I think that you're trying to convince OP to that viewpoint here, rather than answering OP's question.  The rest of your answer is probably within the "how can I make the most of it", but I don't find this part constructive.

@Joe A scientist should ensure that other scientists can reproduce his/her work. This answer points into the same direction as the Open Access discussion. One could even see it as unethical, when only scientists with 'enough money' can reproduce results.

@daniel.neumann Then all science is unethical, because all science can only be done by people with enough money to buy the necessary equipment.

@DavidRicherby Good point :-)

@DavidRicherby There is a difference between choosing a tool because this is the only tool that can solve a problem, and choosing a tool because i feel like using it, though there are other options. Later can be unethical if someone locks out others from reproducing his research, just because he felt so. Former is an unavoidable situation.

@Greg Agreed. That was probably the idea Daniel was trying to get across.

Tool development (perhaps on top of some open codebase) could be an important part of your training (and mark) in many fields. The supervisor also has to be able to supervise the project, and if they're not familiar with your choice of software but you ask for help, guess who's stuck -- you.  That's two reasons why it may be in the interests of a typical student to learn to stitch together the standard tools.
It's not an exact match because of the licence costs and other factors, but if someone started on a project I help run and then said "actually I don't want to write it in Python, I want to use Labview" they wouldn't get very far (their bit can be done in about 100 lines, most is handled by library/demo code).
In response to some of your comments: Viewers are available free would be a huge red flag to me, indicating a company that tries to suck you into a commitment to their software.  Research is based on building on each other's work. If the research group only view your work in the future (and only while the software company supports it) the group is effectively committing do doing the same work again or paying for a licence if any changes need to be made.  By not working with the academic standard software you're doing your colleagues and yourself a disservice.  Sometimes commercial, even expensive, software is standard in academia, so I'm not saying we should always use FOSS, but we should be careful.

I don't think that you're going to persuade your supervisor here. There are two kinds of arguments that you can make.
One is that you are entitled to use the software of your choosing. I don't think that this is true and even if it is, then it's not worth the fight. Your relationship with your supervisor will be strained from the get go. You're better off doing what is asked of you and re-doing the analysis in the commercial software to learn how to use the commercial software. This will cost you less time and energy.
The other argument is that you have to convince your supervisor that is in his best interest. I don't think that that is true here. It will be more work for him to build on your work and to supervise your work. And I don't think that you can compensate him for it any shape or form. Again I would suggest learning how to use the commercial software on your own time.
There is the additional point that learning how to code up the analysis is a valuable skill and exercise. It will teach you a lot about what you're doing and this will make writing up your work a lot easier. In addition, it is also a valuable skill to have in the market place. Not because you can code, but because it's another way of becoming more experienced in breaking down a problem into small parts so that a computer can solve these. The breaking down of a problem is what is valuable.
Now I might be wrong about you being able to convince your supervisor. But if you really want to then you have to ask yourself how he will benefit from it. If he won't, then I don't see how you are going to make him happy. My advice is therefore to learn how to use the commercial software in your free time.

If I were your supervisor, not only would you not be allowed to use commercial software for which my lab doesn't have a license, I'd also likely discourage you from using tools or libraries that aren't ones commonly used by the lab.
Why?
Because research software is a living thing. You're viewing this project as "I finish it, I get a job, and away I go." But if this is intended for anything other than a closed, one-off project that will be entirely wrapped up the moment you leave, research software has to be usable and maintainable into the future. Your supervisor has to be able to look at the project and understand what's been done. They may need to extend it, etc.
There's also some red flags for me in your question:

As I know which tools are used in the kind of jobs I want to get in, I
  do not need the supervisor "to guide my software decisions" to help me
  in this aspect.

There are aspects to any project beyond "Can Unit Root get a job?", and you seem to be utterly ignoring all of them. That's not a great perspective to have when joining a research group.

I am also already quite proficient in one of the commercial software
  tools I want to use, but I feel my supervisor is not (and also has no
  interest in learning more about it - I do not blame him for this).

You are setting yourself up for a situation where if you run into problems (hint: it's a research project, you will run into problems) your supervisor will either be unable to assist you, or it will be a great deal of work for them to do so. The reasons why this might be a bad thing should be obvious. And this may occur even if you are very proficient in the use of software - one of the most fiendish problems to solve in my PhD work emerged from software I had been using successfully for 5 years.

When signing up for the project, usage of commercial software was not
  explicitly excluded.

Approaching this like it's some sort of contractual arrangement with clearly defined terms and conditions is not likely to be a productive way to manage a relationship with your supervisor.
The short of it?

How might I persuade them to change their view? If impossible, how can I make the most of this situation?

You shouldn't. You should do as they ask, do the research, and expand the breadth of your experiences.

Unless I've missed something, you haven't mentioned what the subject matter of your Masters is. It may be that your supervisor wishes you to develop some software that does some specific job, in which case the use of commericial software is inappropriate.
At my institution where I am studying a masters in applied maths, I had the choice of using C programming language, FORTRAN, Python, Maple, Matlab or Mathematica. The advantage of C was that I have a linux machine at home with lots of free software. Unfortunately at university if I wanted to use C I had to make use of Cygwin at university and had problems doing some of the things I needed to do so I eventually opted for Maple.
In part this was because one of my modules was Maple. As well, because my supervisor made use of Maple, if there were any programming issues I could approach him.

Writing code, even if it "reinvents the wheel" also proves you have true understanding of the principles and theory involved, something that often is not necessarily true for a tool operator (even a solvent one). The goal might be not only to get the job done, but to demonstrate you've gone through it following a methodical, rigorous and valid path.
For the project, you should do as your supervisor asked you.

Reinventing the wheel is okay if you're doing a coding class. For a research project it's usually a waste of time (unless the research goal is replication).

My experience is that most terms of use agreements for student versions do not include most forms of research, and are often limited to coursework.  If you go through the terms of use for what you want to use, and it doesn't allow research, you should reconsider your position, or convince your supervisor to buy a full license if it would increase lab productivity.

You can propose to write your project in both the supervisor's preferred software (which you'll have to learn) and your preferred software at about the same time. Assuming that the bulk of the difficulty of your project is in what you're doing with the software, rather than how you do it, then keeping both versions in sync should be reasonable. The flexibility this approach would demonstrate might even look good on a resume/CV. In the worst case, you can simply use your preferred software on the side, for your own benefit, without needing to tell your supervisor.

You can argue that you are not very proficient in the standard software, and if your supervisor wants you to use it they should send you on an intensive training course funded from your research budget. Highlight how much valuable time will be spent by you learning to do the same things all over again in different software, therefore contributing nothing towards your project.
Also investigate whether your data or calculations can be converted to a more open format from the commercial software (in an example from CAD, your colleagues might not be able to use a SolidWorks file but a STEP or IGES is readable by most CAD software). That might be a good compromise.

Instead of arguing it this way if your supervisor wants you to use it they should send you on an intensive training course funded from your research budget.; it's better to make it a request. What do you say?

@Coder That might be the more friendly option, but if there's pushback (these things are often expensive after all) it might become an argument. You'd need to stress how much of a delay learning the new software would have on your project. It's in everybody's best interest that you don't spend weeks struggling to learn (possibly a less user-friendly and intuitive) software.


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How do I stay motivated with repetitive tasks as an undergraduate research assistant?
In a nutshell, I'm drawing circles on images for most of my day (more precisely, ROIs around cellular components in fluorescence imaging). I volunteer to do this on weekdays from 10am to 7pm, and I stay late until 9pm once or twice a week to finish the day's set of images when it's considerably large.
I'm spending at least 45 hours per week drawing circles. I'm working efficiently (it takes me on average of 15 minutes per page of stitched images), I try not to take breaks to maintain momentum unless I'm noticeably slowing down (and limit them to 10 minutes), and I try not to take more than 30 minutes for lunch.
I understand that monotonous tasks are a key part of research, and it's suitable work for me as an undergraduate (as they're low-risk and require little experience). I'm also lucky to do research so early in my career. But in the evenings, I begin to think of all the other undergraduates out there getting ahead doing amazing work (like Martin McLaughlin, who already produced publishable, original work in his first year), and I feel discouraged and expendable.
And it's entirely my fault, too. If I spent my time in high school more effectively by learning Python coding for automation, statistics, and understanding more of the relevant literature, I could be so much more useful to my supervisor doing more stimulating complex tasks.
It's been a month since I've started, and the long hours of this repetitive task are wearing me down. But I don't want to let my supervisor down, so I intend to keep getting the daily image set done each day. She hasn't required me to set these hours or get the image set done each day, but I've been doing this for so long that it's expected (though she's always very appreciative each time I submit, and she works longer hours than me).
I plan to continue until the project is complete when my supervisor graduates in December (lessening hours to the evenings when classes resume). Until then and for future research opportunities, how can I keep myself motivated with monotonous tasks and avoid burning out?

I don't know about your specific task, but drawing circles full-time for a month (assuming it takes no intellectual effort) is a red-flag, even if you are an undergraduate student. And please note that abusing undergrads for lackluster tasks is common in academia.

It's a red-flag for undergraduates, but it's the only task I'm qualified to do as I'm entering my first year of undergrad only next year (hence why I feel lucky to be doing research in the first place). I do understand it's quite common, though this question here suggests it's not unethical. And no, it doesn't take intellectual effort (it just takes pattern recognition to identify the organelles to circle).

I don't know why are you spending 45 hours a week drawing circles, but I am sure that it will be much more beneficial for you rather that time learning. Academically or personally

@user2173836 that was baffling me, too. 45 hrs a week one can learn a lot, a can be useful. If he wants to learn Python, as he says, he can be a functional beginner in a couple of days and start automate many of this

First of all, I think you're taking the wrong approach here. Drawing circles isn't helping you at all in any way. You can't put on your resume that you know how to draw circles. You aren't getting paid. You aren't learning anything. You're burning yourself out by working 45 hours a week and you haven't even started university yet.
In my opinion this is a perfect opportunity to learn programming and image processing. I have worked with many undergraduate and even high school students (I was one myself) in different labs, and I can tell you that you're perfectly capable of learning basic programming skills over the next two months if you work at it. With these skills you can attempt to make software that recognizes these ROIs in your images automatically.
From the sound of it your supervisor is a graduate student and not a professor, and since you're volunteering, they should have no problem with you taking a different approach to solve the problem of identifying ROIs. If they want people to do simple repetitive work, they can use a service like Amazon Mechanical Turk.
So to answer your question, academia is all about coming up with new approaches to solve problems or learn new things. If you want to stay motivated, use this time to learn something new that will help you in the future, and also help your supervisor.

You know, you're right! Thank you for encouraging me and giving me a practical solution. I'll get back to reading Guttag's Introduction to Computation today, and I'll work myself up to implementing something with OpenCV. Even if it doesn't work, it'll certainly be a transferable skill.

@user234213234 Programming experience in Biology will be extremely helpful if you plan to stay in academia. While you read that book, here are some Python packages that would be helpful to be familiar with: numpy, matplotlib (for quick graphs/plots), scikit-image, scikit-learn, and opencv.

Thank you for taking the time to write out that very useful list! I'll aim to learn each one over the next couple of months - I really appreciate your help.

@user234213234 No problem. And don't forget that you likely won't come up with a solution that works perfectly, and that's to be expected for anyone who does image processing. Even if your code only works 70% of the time, that's 70% less manual selection work you have to do.

Another alternative for this task is to become familiar with ImageJ. ImageJ is free image processing software developed with US NIH funding. There are dozens of plugins for ImageJ to do image segmentation, specifically for people tired of drawing circles.

You need to first be clear with yourself about your expectations of your volunteer activity and then communicate it with your supervisor or maybe the lab investigator. She may suggest you to work on a more intellectually demanding project after you finished your current task (hopefully soon). If not, you can ask her to design a better plan for your research activity in the lab that satisfies your exceptions in addition to the lab's. At the end of the day, you may decide to stop your activity for now and focus on your studies for some years. Doing high impact research needs a solid foundation of the research area which can be obtained through taking different courses in your major. after a while, you would have more knowledge to be able to work on a real project with more challenging tasks and with a more distant supervision. In my experience,  Having a full focus on your courses for now can guarantee a more productive research experience in future for you.


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Is there a journal or 'place' to publish poems written by and for other researcher in the same field?
I've seen poems squeezed in-between chapters in books, but I don't want to write a book for each poem :-) . Hence my question:
Is there a journal or 'place' to publish poems written by and for other researcher in the same field?
What I have in mind is for example a poem written for physicists.

On your personal website or in a normal poetry anthology are two possibilities I can think of.

Write your own book and put them in there?

There might be a blog.

Web of Science indexed 4,117 "poetry" items in 2017 - they do all indeed seem to be poetry rather than critical works. On the other hand, they're almost all in literary journals, but there was one in the Australasian Journal of Information Systems and another was in the Journal of Palliative Medicine...

In mathematics, the Mathematical Association of America has several journals aimed at undergraduate students (which many researchers also read): the American Mathematical Monthly, College Mathematics Journal, and Mathematics Magazine.  All of them regularly publish short poems related to math. (Often they appear in the otherwise empty space on the last page of a regular article).

Some scientific journals publish letters to the editor that may include jokes, anecdotes, and even poetry.  The New England Journal of Medicine has traditionally been notable for the humor and literary quality of its letters column.
In physics, the American Journal of Physics used to publish short humorous letters of this type.  (I recall one letter from David Mermin setting out the absurd theory that Newton's use of "p" for momentum was an abbreviation for "pimento.")  However, it seems that they may not publish such items any longer.

The Journal of Humanistic Mathematics has sections called Poetry Folder and Poetry.
From their website (emphasis mine):

We publish articles that focus mainly on the doing of mathematics, the teaching of mathematics, and the living of mathematics. We also welcome contributions about the state of the mathematical profession (both in research and in education), underrepresentation issues within the world of mathematics, mathematics across national and cultural boundaries, mathematical fiction and poetry, personal reflections that provide insight to the inner workings of the mathematical mind, and other types of writing which may stimulate discussion among our readers. Overall we are a free platform where many different conversations about mathematics are welcome and encouraged.

Poetry is for everyone!
If you're in a university, get in touch with your arts and humanities faculty for advice or even potential collaboration. I am sure there would be interest.
Of course, you could also publish your own book in print or share online via a blog.
But if you're interested in reaching a particular audience in your field, you can always informally contact the editors of a journal you know to see if they would want to share your poetry in spare pages of an issue. I've not seem in it in the hard sciences, but occasionally see this sort of thing in arts, humanities and social sciences journals.
On the topic of poetry and physics, many winters ago I was taught by Mario Petrucci, the author of a poetry anthology that used imagery from nuclear physics as a motif to articulate the tragedy of Chernobyl:
Petrucci, M. (2004) Heavy Water


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Job prospects in case of an unwelcoming mentor
A friend of mine, let's call him Jim, is a postdoc in Germany. Jim's contract is ending soon, and he talks to me often about this issue, so I decided to ask here. (Perhaps, this community can provide a piece of advice though I'm not directly involved.)
Jim publishes about one paper per year in a high-rank computer science conference or journal and does some teaching (seminars + teaching assistant for a lecture or teaching assistant in charge of a lecture). Otherwise, he is completely clean (no academic fraud, no convictions).
As far as I understand, Jim failed to integrate himself into the current research lab at a university paying him. (Probably, Jim took way more time than he expected to publish on his old topics unrelated to the activity of the lab and, AFAIK, is still not fully done with it.)  Jim did everything necessary for the project which he was working on in this group and for required teaching; but the project ran out, and now the head of the group seems to try to get rid of Jim as soon as possible. The head is not very welcoming: the head does not finance conference travel despite earlier promises and does not answer e-mails.
So, given the fact that Jim is starting to apply for other positions, what are his chances on the job market in 1st world developed countries (North America, Western Europe, Israel, Australia, Japan, ...) where a good command of English and German is actually sufficient to live? It's not his first postdoc position, and it is not known whether Jim's current mentor (= the head of the lab) would actually send any reference letters for Jim at all when asked. How would Jim approach applying for tenure-track academic positions (or even industrial positions) if it is not known whether any reference letters would be actually sent out? (At certain stages, which is 1.5 till 5 years back, all Jim's previous mentors have confirmed to him that they will send the reference letters, but Jim is not sure whether they would actually send the letters, and Jim seems to have no chance even to find out whether the reference letters have really been sent or not.) What incentives (that Jim could trigger now) could cause a previous mentor to actually send a reference letter rather than simply replying "done" or moving the request to the trash bin? The situation is exacerbated by the fact that Jim promised to never ask for any reference letter from his PhD advisor. (It was a private promise for some private reasons, but still a valid one. Perhaps, Jim overestimated himself in the past or the like.) Even if all the prior mentors (except the PhD advisor and the current one), which are two or three, do actually send reference letters, but the current one is excluded, would it be worth to apply?
Each proper job application for a tenure-track position takes Jim a couple of full working days, so he is not wishing to invest his time into something which is doomed to fail.

Comments are not for extended discussion; this conversation has been moved to chat.

My experience in Europe has been that the current boss / mentor is not necessary as reference. I have recently switched jobs, and I have been told privately that they decided aginst even contacting my previous employer, as he would be biased one way or another anyway. I think just not having a reference from his current postdoc advisor is in no way a reason not do go on the job market.

Jim seems to have no chance even to find out whether the reference letters have really been sent or not — At least in the US, departments are generally willing to confirm that applications are complete (meaning all letters have been received).  Also, many US CS departments use letter services like Interfolio, which can send receipts to applicants when their references submit letters.

Having a strained relationship with his past mentors (both PhD and postdoc) is definitely going to put Jim at a disadvantage on the job market.  But that doesn't mean he has no chance at finding a decent faculty position.  Here's what I would recommend.  This is aimed at looking for faculty positions in the US, where recommendation letters are mandatory and crucial; hiring practices in other countries are different.

Ask directly. Worrying that the supervisor won't send letters or won't write a strong letter is pointless.  Jim must ask his supervisor directly, in person, face to face, if they are willing to provide a strong letter of recommendation.  He should also make it clear that to simplify their work and preserve his sanity, he will provide a mechanism to track letter requests (see next).  If the supervisor agrees, Jim should immediately send email confirming the agreement.
Track letter requests.  Jim should provide an online spreadsheet (via Google Docs, for example) that lists all the positions Jim has applied to, one per row, with contact information and deadlines, and a column for each reference.  Then references can indicate in their column which letters they have sent and when.  Tracking not only relieves Jim's uncertainty; it also drastically simplifies the job of his references.  It also provides a public shaming mechanism, since Jim and all his references can see who has or hasn't sent which letters.  (This is not just a suggestions for Jim; everyone on the academic job market should do this.)
Use a letter service like https://www.interfolio.com/ or https://academicjobsonline.org/ , which allow applicants to track the status of letter requests, and provide interfaces for references to upload confidential (generic) letters and for departments to retrieve them directly.  Again, this both lowers stress for the applicant and simplifies the work of the references.  Not all departments trust these services—some people prefer to communicate directly with references—so this can't be the only tracking mechanism.  On the other hand, some departments actually require using these services, so Jim may as well use them anyway.
Double-check with departments. If Jim is really worried that his supervisor is lying when he says he's provided the letter, he should ask a few departments to confirm that they have received all their requested letters.  Not all will reply, and some departments may be vague (because they need to keep confidential whether they've requested letters at all, or which of your N references they've asked), but enough will reply that Jim can either rest easy or know for sure that his supervisor is a dishonest jerk.  (In that case, Jim should update the tracking spreadsheet to indicate which letters were "sent" but not actually received.)
Find good references from the research community.  Since Jim already has several years of postdoc experience and a nontrivial publication record ("one paper per year in a high-rank computer science conference or journal"), he is already known in his research community through his work.  At this point in his academic career, most of Jim's references should not be supervisors, coauthors, or other faculty at his previous institutions they should be arms-length experts in his field who can give an independent evaluation of his research record.  Jim should ask for letters from experts who have given him positive feedback in the past, either by citing and building on his work, or by offering supporting comments in person at conferences.  (Ideally, Jim started cultivating these outside experts as potential references when he was still a PhD student, but better late than never.)  Remember that a normal part of asking for references is asking for suggestions for where to apply.
Have more references than required.  Most US departments ask for three recommendation letters.  Under normal circumstances, I'd suggest finding at least four references, so if someone doesn't reply you have a backup.  If Jim is worried that some references won't actually send letters, he should find five.  (That said, some departments only allow applicants to specify three references, or only request letters from the first three of N the applicant provides, so it's important to prioritize.)
Apply broadly. The application process is random; crudely, the most lottery tickets you buy, the more likely you are to win.  Not having a letter from his most recent survey would be a red flag, but that just lowers the chances of any particular application panning out.  Jim can counter that effect by applying to more positions.

What incentives could cause a previous mentor to actually send a reference letter rather than simply replying "done" or moving the request to the trash bin?

Professional embarrassment.  After all, your other references will know that he agreed to write letters for you.  Being known as a dishonest jerk will not be good for Jim's supervisor's career.

Each proper job application for a tenure-track position takes Jim a couple of full working days, so he is not wishing to invest his time into something which is doomed to fail.

It really shouldn't take that long, at least for tenure-track positions at US research universities.  Most of the successful faculty applications I see (in 15+ years on my department's hiring committee) are at most minimally tailored to my department, except possibly for the cover letter (which almost nobody reads).  In particular, the CV should be a complete record, and therefore identical for every application except possibly for order: research first for research-focused positions, teaching first for teaching-focused positions.  The research and teaching statements should confidently focus on Jim's accomplishments and vision.  Uploading the documents should only take a few minutes.


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What can a student in England do, if her Disability Office refuses PDF versions of textbooks?
My sister is an undergraduate at a university in England, and emailed its Disability Office  (let me abbreviate this to DO) a letter from her physician stating that disability thwarts her from carrying books (like her many heavy textbooks), because a publisher suggested PDF Accessible Formats of books that she must request through her university's DO.
But the Head of DO informed my sister that he doesn't consider her to have 'print disability' or to qualify for PDFs, probably (we are guessing) because he doesn't want to spend time obtaining the PDFs for her. He has offered nothing else useful for her.
We think that he's wrong, but how can she acquire the PDFs?

Has the student asked the disability services office what kind of documentation would be required to qualify for PDFs?

@ff524 The Head didn't say anything about the letter and we haven't asked because the letter makes the disability obvious, but thanks! We'll ask tomorrow.

There are typically different channels people can use to raise issues or make complaints, such as tutors, ombudsmen, student support office, student mentors / representatives, even a friendly lecturer.

Even if the disability is obvious, the necessities needed to accommodate for it might not be obvious to everyone, even a disability office. There are many types of disabilities and they come in different severities (and different humans anyway need different things to help them).

'He has offered nothing else useful for her.' Note that a letter from your GP is not usually sufficient to get disability support. Typically the DO can only provide specific accommodation to students following an assessment from one of a small list of providers. The accommodation offered is then directly linked to that assessment, in pre-defined categories.

I have an alternative take on the circumstances.
From Wikipedia, a Print disability refers to an impediment that prevents the reading of printed material. Presumably, the PDFs the disability office has are intended for students that need to use some other method, for example: 1) a text-to-speech program, which can't operate on the printed books, or 2) a digital display for a student with a disability that prevents them from turning pages.
It sounds like your sister has trouble carrying physically demanding loads, like a heavy textbook, but that doesn't mean she can't read a textbook that is sitting in front of her on a table. If this is correct, indeed your sister may not meet the definition of "print disability" that the DO is using.
Although the publisher sent your sister to the DO to obtain PDFs, they probably want no part in assessing whether the accommodations are necessary, they are punting it to the DO. The DO, on the other hand, might have a specific licensing agreement with the publisher that only allows them to provide digital copies if certain criteria are met under their definition of "print disability." It is possible that difficulty with the weight of a textbook doesn't fall under their terms.
I would suggest meeting again with the DO before escalating this to other offices, explain the nature of the disability, and see what accommodations can be made. Personally, when I was an undergraduate student carrying around heavy textbooks just wasn't a good idea for anybody. They were rarely actually needed in a course, they were used at home. It might be that the DO would rather provide a physical textbook copy in courses where a physical copy is needed in-class on a course-by-course basis, rather than providing PDFs (which they may not have a legal right to distribute).
Alternatively, as others have suggested, your sister could obtain digital copies on her own if possible.
(just to add: I think it's unfortunate, to say the least, that the DO didn't directly suggest other accommodations. You have a right to be frustrated by that, but I would try to be polite in the short term and try to assume that the DO head is simply busy rather than negligent. DO's could very easily be understaffed. Maybe they truly are just a jerk, but if they aren't and you assume they are, it will make the situation more difficult for everyone. Assume the best, try to be proactive, try to be assertive without being demanding, etc.)

Disclaimer: I have some experience with a similar office in my university  but this is based on just one university. I'm also not from the UK so i do not know the legal situation and I do not know the policies of your university. This also just my opinion, not legal advice.
However there seem to be three scenarios:

The university does not recognize your disability as a disability or does not acknowledge its effects. In this case you should first try to get the university to accept your disability. Without this acceptance getting the university to do anything will be hard. You might ask specific teachers to do this for you or other nice people but in general this will be difficult,except for suing the university which I think is probably not a great solution ( unless it is obvious the university should recognize your disability. ).
The university does recognize your disability but does not provide books for any students. In this case it becomes complicated because you usually only get help with services that the university normally provides, That is you do get help (at least in my university) if because of a disability you cannot read your exam because the font is too small (you'll get larger fonts and usually the size of the paper is also bigger). However if you want something the university does not provide it is much harder to get, for example you cannot use the standard calculator because of the exact same reason. However since the calculators are never provided by the university it is hard to get a larger calculator. However you can still try to get it if it is truly unreasonable if you don't get it but your position is much weaker.
Finally if the university does recognize your disability and normally does provide the books, then it is likely that they are required to provide it for you. If there is an ombudsman than you should probably try to contact him/her to address this.

In general if the bureaucracy does not cooperate or is very slow, you might just want to contact the teachers directly. Most teachers are quite understanding and if they can do so easily will provide you with what you need. You can also try to buy the books as e-books. or contact the author and ask him for a digital version.

There are several routes to resolving this:

Your sister should contact her lecturers or her tutor, and tell them how unhelpful the disability office has been. They may be able to escalate this issue. Alternatively, they might be able to procure the PDF versions of the textbooks.
Your sister should contact her student union. Most student unions have a disability officer who has been elected to represent students with disabilities. They will be able to intervene on your sister's behalf.
Your sister can make an complaint about her treatment by the disability office. She would first need to make an internal complaint. Her tutor or disability officer would likely be able to help with this. If this doesn't resolve the issue, she can complain to the Office of the Independent Adjudicator. Disability Rights UK has further information about making a complaint.