text:
Omission of contributing author
I worked at an institution on a project for 5 years. The type of project I worked on usually results in a single published paper at the end of it. However, I left the institution before the project's end.
I now find out the PI has published the paper (2 years after my departure) with a long list of authors who have spent far less time working on the project than myself.
Upon contacting the PI (lead author), they said that I was out of contact after I left the institution and:

Since publication requires the agreement of all co-authors, we could not add on anyone who we could not contact. As we were preparing the paper, the project manager tried to contact you in various ways, all without success. As a result, we could not add you as a co-author.

Note1: It appears they do not dispute my contribution or authorship!

Note2: I have an email exchange with the project manager 1.5 years before paper submission, and an email exchange with the PI 1 month after paper acceptance which is 7 months before paper publication. In neither of those exchanges the paper submission is mentioned. Nor did I receive any emails regarding the paper from them. I suspect they did not try to contact me at all regarding the paper!

My questions are,

Can lack of contact be a valid reason not to include the name of an author during submission?
Can the list of authors be amended now, after publication, to include myself? And how can this be done?
Is omitting an author considered a 'Scientific misconduct' or 'plagiarism'?

Edit:

I am not in academica anymore
I want my name on the paper as I have spent five years of my life on this project.
Before I leave I sent every one my gmail account as a forwarding address. And all my subsequent exchanges was and is with the same gmail address.

Are you still in academia? What do you want to happen? Is your institutional email still active? (i.e. what email did you use to talk to the PI after the paper acceptance?)

Did they have your email after you left? Maybe they tried to reach you and were unable? Since journals demand all named authors to actively agree on a publication, a named author having gone off-grid might block a publication.

I beleive I have met the criteria for authorship as the PIs email does not dispute authorship but lack of contact.

What gets me is a month after paper acceptance, I contacted the PI and he replied to my email without mentioning the paper nor his efforts of trying to contact me. This is still  7 months before publication!!!

If someone has done enough work to qualify as an author if they would only complete some late-stage steps like helping to draft the manuscript/review the final manuscript, then their coauthors have a duty to offer that person to be included in those steps. It's not fair to purposefully prevent someone from fulfilling a key criteria for authorship in order to leave them off the list.
However, I do not think it's reasonable to expect that coauthors not publish work because they cannot reach a colleague who has completed some but not all requirements for authorship. They should possibly be acknowledged instead, though some are also concerned about acknowledging people without their permission.
It's not clear what exactly has happened here. It seems you did not receive any contact, but it's hard to judge the scope of the effort that was made to contact you. Given you did have contact with the person who supposedly reached out to you both before the acceptance and with the PI afterwards, it seems they were aware of contact information that could reach you. I agree that makes things suspicious, but maybe less so if, for example, the latter exchange was initiated by you rather than the PI, and if the former exchange was over an email address you no longer use.
It's unlikely the list of authors can be amended except by some serious steps likely involving retracting the original paper. Yes, it would be academic misconduct to leave an author off, but you should think carefully about what your goals are in pursuing this serious accusation. I'd start by asking what methods were used to contact you, given your previous email contacts with the project manager.

Papers are digital now a days, why would you say its unlickly that a name can not be added to the list of authors?

@SpaceSailor That's just not how most journals work, once something is published it's published, they don't keep making edits and tracking versions.

Not in and of itself. However, if you're hard to contact, it might motivate people to change the paper so that it no longer contains any contributions from you, and ship that paper, without you on it. That's reasonable, if none of your work went into the modified paper. What they shouldn't do is write papers that involve your contributions without your say-so and without including you as an author - that's misconduct.

Doubtful, even if the paper does include your contributions. If it does, and you're willing to pursue the nuclear option, you could in principle write to the editor of the journal and ask them to retract the paper. That may or may not work, but will make the PI hate you, if you still care. It also still won't get you on the paper (that ship has likely sailed).

Not giving authorship to someone whose contributions have met the threshold for authorship (assuming yours have) is scientific misconduct. It's not plagiarism - they didn't copy text you'd published in another paper.

For what it's worth, I would have some sympathy for your former lab in at least the following situations:

The paper depends at least somewhat on your contributions (you meet the threshold for co-authorship). They try repeatedly to contact you, but you don't bother to reply to them. They have no prior reason to think you wouldn't want the paper published, and it's to your benefit if it is published. They publish the paper, giving you appropriate credit for your contributions. This isn't great behaviour as far as the wider community is concerned (*), because it misrepresents your involvement in the paper and willingness to take responsibility for it, but I would have some sympathy for them - they were at least trying to do the right thing by you, even though you caused them a problem.

A paper can be written that doesn't rely on your contributions. Having not heard back from you, they publish it, without you as a co-author. You feel annoyed because you did a lot of work that could have gone into the paper and made it better, but it didn't. In this situation, they haven't done anything formally wrong. Maybe you could have replied, maybe they didn't try hard enough to contact you, whatever, but they're in the clear. You and they might need to work out some issues, but it's not a problem for the wider community to solve.

(*) Which is to say, you should avoid doing this yourself. It's particularly egregious in certain fields, e.g. medical ones, but bad behaviour in any field. That said, I would personally feel a bit sorry for them because of the situation you'd put them in.

My main motivation is to for my name to get included and not the nuclear option as you put it. And why would you say that, that ship has sailed, surley papers are digital now a days and adding a name cannot be that dificult.

@SpaceSailor: Yes, it makes sense to want that - but unfortunately most journals (as a matter of policy) refuse to add authors after the paper has been published, and most editors are less than keen to take sides in disputes like these. If you really kick up a stink, they might retract the paper, but that doesn't do much for you personally sadly.

Inclusion as an author of a paper is field- and research-group-dependent. Here is one example from Oceanography, which suggests a "2 out of 3" rule, where you are expected to contribute to two out of three of (1) ideas, (2) analyses, and (3) writing to be considered for authorship.
Although you don't provide enough detail to understand the circumstances of your case, it sounds like there was an expectation but no official written policy for what level of contribution was expected to be included as an author. It also sounds like you didn't know in advance what would happen if you left the project before it was finished. If you're still in academia, I would suggest this is a lesson for the future, and you should always know what is the publication policy for your research group. Without having a clear policy, it is difficult to answer your questions (1) or (3), but in general it is not reasonable to expect that research would remain unpublished if somebody who contributed just drops out of the face of the earth (I'm not saying you did, but they are saying you did). The show must go on, etc.
For the specifics of your case, and if you wanted to press the case further, you could ask the PI for the evidence that they tried to contact you about the paper (surely they'd have an email), and/or you could contact the editor of the journal with this grievance, but I suspect it is highly unlikely your name could be added to the paper once published.

It's not reasonable to expect that the research would remain unpublished, but it is reasonable to expect to be given co-authorship of the publication if the paper makes use of your contributions to the extent that you've met the usual threshold for co-authorship. It's not clear whether that test has been met in this case or not.

@StuartGolodetz, yes, that's what I wrote.


text:
Reply to desk rejection?
I recently got a desk rejection for a paper submitted to a journal. It was about as generic as a desk rejection form response can get: an "outside the scope of this journal" response; no personalized feedback at all. I was wondering whether to send a brief, polite thank-you.
I have searched around the Internet, and it seems opinions are kind of split with a slim majority saying if it's a desk rejection, don't respond at all. Some who advocate for that are quite adamant, saying it would be an inbox nightmare for editors if every desk rejectee sent a response, no matter how brief. But there were a few on the other side, saying it's always a good idea to send a (very brief) thank-you.
The boiler-plate response I got said that the journal hoped this would not discourage me from making future submissions. I was wondering if there have been any published surveys of journal editorial staff querying their reactions to replies to desk rejections. Does it affect their decision-making in future submissions from the same author?
Thank you very much.

I think all you will get is opinions.

There is no upside.  The editor will not be your friend.

It does not matter.  There is no etiquette requirement that you should do so, but neither would it be unduly rude to send a note.
If the editor sees an e-mail from you, coming on the heels of a desk rejection, they will probably be pleasantly surprised when they start reading the e-mail and find that it is a short, polite note of thanks for their work—rather than the bitter complaint e-mail they were expecting.  This might give the editor a quick smile, but you have also used up a certain amount of their time, and the smile will almost certainly be quickly forgotten as they move on with their workload.

This isn't necessary. Once a paper is desk rejected it's out of the journal's hands and likely their minds as well, since they have nothing more to do and are not expecting to have anything more to do.
Such a reply does say you have received the decision, but you kind of must have received the decision, since after all you submitted the paper using that email address. Not to say you can't send such a reply, it's just not necessary. The journal editor is likely to delete such a reply with no response.

Thank you for your feedback. I am leaning towards a very brief thank you note in response.

source: Stack Exchange

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

sort: votes


text:
Should I use strikethrough while the article revision?
I got an email from a reputed journal of Taylor & Francis pointing to the Major Revision of our systematic review article. As an author, I started the revision work by colouring the revised text "Red" and striking through the discarded texts. Now the problem is if I use strikethrough, then neither the word count nor the numbering of headings changes. What do you suggest as altruists? Should I include the strikethrough texts just to show the reviewers that we have made significant changes or just remove them for good?
NB: They mentioned not to use the "Track Changes" function because their system doesn't support that at this moment. And I'm using MS Word to format the manuscript.

Use the markup function.

I forgot to mention that they prohibited to use the "Track Changes" because their system doesn't support this at this moment.

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


text:
Postdocs or RTDa/b positions and a question on PhD acquired outside of Italy and equivalence with the Italian title
Is it necessary to have obtained the "equivalence" of Ph.D. acquired in another country (Germany in my case) to the Italian title before applying for postdocs or RTDa/b positions in Italy?
I found this page about the process. Are there more detailed resources to guide me through the administrative process of requesting the equivalence? Is there anything in particular that I should be careful about?


text:
How do the logistics work for recipients of a DFG "Eigene Stelle" grant (in Germany)?
The Deutsche Forschungsgemeinschaft (DFG), which funds most basic research in Germany, has a grant program that funds a temporary position ("Eigene Stelle") for novice principal investigators (PIs) who have completed their PhD.  I have several questions about how the logistics would work if I win such a grant:

How does the salary work? Is the salary negotiated with the host university or with the DFG directly?
Who is the additional funding (travel, workshops, etc) given to? The PI directly or the host university?
Is it possible to leave the position months before the scheduled end of the project? For example, in case of an employment offer elsewhere or are there any penalties?
Are there any publicly available (successful) project proposals?

Concerning the first bullet point: There is nothing to negotiate: Salaries are determined by a collective wage agreement (Tarifvertrag) for public servants.

@JochenGlueck Isn't there wiggle room betwen E13 and E14 in this context?

@user934318: Ah ok, that might be right. According to the first paragraph in this DFG document the decision whether you get E13 or E14 is done by our employer (i.e., the university). Now I'm not sure how much room for negotation there is with respect to this decision.

@Roland Thanks. I see, but is there a chance that the DFG will ask for a refund on the funds provided for the whole duration of the contract?

Even if it sounds so, DFG "Eigene Stelle" does not fund you personally. You wouldn't even be considered a viable PI without being associated to a university with support from an institute. In Germany, if you do not have full support of at least one full professors, any grant application is almost impossible.
So, you don't negotiate with DFG. The money is given to your university/institute and you negotiate with them. In Germany this is the well known "öffentlicher Dienst" with all its standard tables. No exceptions.
Also all additional money goes to the institution. If they manage this properly, you will get your own "Kostenstelle" where you book your expenses in a self organized way. This is the typical way to access grant money. However, if the institute would get in significant financial trouble -- your grant will be affect together with it (not a very likely scenario, but illustrating where the money actually sits).
You can always leave. But you can't take the grant with you. There are other (much more personal) grants like Helhmoltz Young Investigator, DFG Emmy Noether, ERC starting grant, where you can well negotiate and move around to different places. But certainly not with DFG "Eigene Stelle".
There is no public database with proposals. Proposals are always confidential and are not going to made public. Often there are new ideas in them, right... This is somehow the entire idea of it. You have to know someone who trusts you and shows you his proposal.
Additional details

How does the TV-L 13 vs TV-L 14 negotiation with the university work?

The actual table is here: https://oeffentlicher-dienst.info/tv-l/allg/
You will have to negotiate the "group/level" 13/14 with your supervisor, most likely this is the institute leader. It depends on the institute structure and your own future plans if this will be successful. The "group/level" negotiation is a strategic one.
But besides the "group/level" there is also the "step" which only depends on time/experience. The "step" you have to negotiate with the human resources department, you will have to prove them "experience in years" so they will put you in a higher "step". If you are young, this is difficult and you may just end up in "step" 1. The "step" negotiation is very technical and super-bureaucratic.

Could you elaborate on how the "Kostenstelle" works in this context?

That's just bookkeeping. "Kostenstelle" is a dedicated (bank) account for your project. It is very good to have your own account, it gives you a lot of freedom. But also responsibility.

If I already have a postdoctoral contract with the target university for the DFG project, what should the "employer authorization/availability" for the DFG application say?

You still need official support from the institute granting you office space and working material, computing, lab-space, as well as integration into the institute. Without an institute to support you, you can't get an "Eigene Stelle".  It is not enough to point to an existing contract since times may differ, and also the project may change, etc.

Is it 100% sure that there is no money-back policy if I don't stay for a certain percentage of the scheduled contract duration? For some European funds, I know that if you quit before 80% of the contract duration is completed, you have to give back all the money you received.

This is not 100% sure. But I would be extremely surprised. Maybe someone else knows? But why not just write a mail to DFG. They will tell you. There is a dedicated person responsible for you at DFG (depending on your research topic)...

If not the fille in proposal, are at least the proposal modules available online (without actually starting an online application)?

I guess you mean this:
https://www.dfg.de/foerderung/programme/einzelfoerderung/sachbeihilfe/formulare_merkblaetter/index.jsp

Is it possible to apply for other types of funds (e.g. ERC, DAAD, etc.) while holding an Eigene Stelle?

Absolutely. I think this is within one of the core ideas to apply for larger grants as follow-up. Of course, with any new application you have to make sure it is not an already existing project, but a new one (follow-up)... Also, avoid "double funding". DFG will not "double fund", thus, if there is already money from a different agency, DFG will not give more to the same research.

True. I mentioned Emmy Noether later, too. I will try to improve this.

Thank you so much for your answer. It's very helpful. (1) Ok, I see. Do you have any information about the TV-L 13 vs TV-L 14 negotiation? Also, is it possible to negotiate additional "perks" with the university? E.g., set up of the office material, vacations, additional bonus, teaching duties, etc? (2) Can you tell me a bit more about what is a "Kostenstelle" and how it works (in general and also specifically in the context of the DFG)?

@user934318: E13 vs. E14 for a novice PI would hinge on whether you look after your own group or not. Holidays are part of the collective agreement (IIRC 26 until you're 30, 29 until you're 40, 30 afterwards)

@Roland and RalfUlrich Thank you! I added a bounty to address some additional details: (1) How does the TV-L 13 vs TV-L 14 negotiation with the university work? (2) Could you elaborate on how the "Kostenstelle" works in this context? (3) If I already have a postdoctoral contract with the target university for the DFG project, what should the "employer authorization/availability" for the DFG application say? (continues...)

(continued) (4) Is it 100% sure that there is no money-back policy if I don't stay for a certain percentage of the scheduled contract duration? For some European funds, I know that if you quit before 80% of the contract duration is completed, you have to give back all the money you received. (5) If not the filled-in proposal, are at least the proposal modules available online (without actually starting an online application)? (6) Is it possible to apply for other types of funds (e.g. ERC, DAAD, etc.) while holding an Eigene Stelle?

@cbeleitesunhappywithSX Concerning TV-L, each employee gets the same amount of holidays since 2012 (30 days, when working 5 days a week) (s. https://www.oeffentlichen-dienst.de/tv-l/urlaub.html).

@erc: thanks for correcting me - I remember that from back then, but did a quick search last week - and apparently ended up in a table for TVL-alt contracts (i.e. old contracts that started before 2012). (I'm not TV-L any more :-) )

Thank you so much! That helps a lot! A few more questions: (1) So, I can apply for future funding while holding the position, but not for simultaneous funding? Or can I apply for simultaneaous funding but for a different research topic? (2) Who will manage the Kostenstelle? Myself or a secretary from the university administration? (3) Should I be specific in the funding request module to fill in that I'd like to apply for E14 level of funding? (4) If I also apply for a DAAD travel grant, is the funding from that in addition or in substitution of the usual TV-L salary?

That last question about DAAD actually also concerns PhD students and postdoc with a TV-L salary but without DFG support. Do you happen to know if the DAAD support is cumulated or substitutes to the salary in those cases?

(1) new funding only has to be "new idea",   (2) I only know the case where a secretary does this  (3) yes, but there are standard numbers for salaries for DFG, https://www.dfg.de/formulare/60_12/60_12_de.pdf    (4)    travel grants are never salaries. You never get such funds on your personal account. Only if you travel for work, you can pay from this. Nothing else. None of the fundings go to your personal account. You always only get TV-L, that's it.

@RalfUlrich Thank you very much! About the DAAD funding, there's another post with links to the specific programs: https://academia.stackexchange.com/questions/175743/daad-funding-for-stay-abroad-for-phd-students-and-postdocs-is-it-added-to-the-r it seems to be a compensation rather than just a "travel refund". What do you think?

@RalfUlrich Among the documents that you linked (https://www.dfg.de/foerderung/programme/einzelfoerderung/sachbeihilfe/formulare_merkblaetter/index.jsp), which one is for specifying E13 vs. E14?

The E13/e14 is in the pdf from the comment section from yesterday. This is german, maybe there also is an english version, but it is just a table. You should be able to understand.

Your second question is answered well in the other answer. I have nothing else to add.


text:
bibtex entries for versions of the c++ standard
Where can I find BibTeX entries that help me cite a version of the C++ standard? In a paper I discuss the necessity of trailing return types, which became available in C++11. I want to be able to cite this version of the standard.
I came across a post on this site here. Adam Erickson's answer provides a link to this page which appears to have entries for all versions of the standard. However, I wonder

if these are "outdated" in some sense because a few of the links are dead; and
which citation I should use (e.g. "ISO:2011:IIIa" or "ISO:2011:IIIb" or ...).

I just had to use a better search query. "cite ISO/IEC 14882:2011" gives as a first result this page: https://www.bibsonomy.org/bibtex/24b660c16d9a5ab0ad595b1555402c797/gron.
Here's the BibTeX entry:
@book{ISO:2012:III,
  added-at = {2012-10-08T01:13:47.000+0200},
  address = {Geneva, Switzerland},
  author = {{ISO}},
  bibdate = {Mon Dec 19 11:12:12 2011},
  bibsource = {http://www.math.utah.edu/pub/tex/bib/isostd.bib},
  biburl = {https://www.bibsonomy.org/bibtex/24b660c16d9a5ab0ad595b1555402c797/gron},
  day = 28,
  interhash = {ff5df6d7fa67f89d7d5ea964dab3e3c9},
  intrahash = {4b660c16d9a5ab0ad595b1555402c797},
  keywords = {C++ Specification Standard},
  month = feb,
  pages = {1338 (est.)},
  publisher = {International Organization for Standardization},
  remark = {Revises ISO/IEC 14882:2003.},
  timestamp = {2012-10-08T01:13:47.000+0200},
  title = {{ISO/IEC 14882:2011 Information technology --- Programming languages --- C++}},
  url = {http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=50372},
  year = 2012
}


text:
Are there any automated ways of getting PDF annotations into Word or LaTeX source code?
With my previous two submissions to Elsevier journals, I have received reviews from 5 and 4 reviewers respectively. This results in a large number of comments that needs to be addressed. Some of the reviewers provide a PDF document with annotations that contain their comments and questions. Are there any automated or systematic ways of transferring these comments into my source code (LaTeX in my case but this question is just as applicable to MS Word) so that I can have a single view of all the comments?

@artificial_moonlet: It is certainly the best option I have been able to come up with. Alas, I am a hacker at heart and dream of automation. I'm just curious if anyone else has approached this problem differently.

If you are on linux, there is a tool called pdfannoteextractor which does what you ask for. But this is probably highly off-topic :)

Hi @nabla, thank you very much. I'll check it out. I think the challenge is to get the annotations into the source code after extracting the annotations.

@artificial_moonlet I agree (and also enjoy xkcd), I was hoping someone else did the legwork, allowing me to be on the right side of the chart.


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What to do if one comes to a realization that research and post graduate studies is not for him/her?
Life doesn't allow for a redo. I have been a decent student in my undergrad and got placed in a reputed company right after graduation. However, research and academia always inspired me. I got into a prestigious school in India for my master's and decided to work on a particular field as part of my thesis. I did not go for hot topics because they didn't interest me.
Subsequently, I went ahead and joined for PhD in the US, on a similar field as my masters. However, after 2nd year, I realized the importance of working on hot topics and how conventional topics struggled to secure funding and permanent positions after graduation.
But, the ship has sailed and I have completed my PhD and soon to start a postdoc. But, I have come to a realization that I have made a career suicide by pursuing post-graduate studies. There's nothing permanent and decent-paying out there for me.
I shouldn't have pursued post-graduate studies. And I feel lost. I don't know what to do next.

You're asking for advice about how to move on to a non-academic career.  Your question would probably be more appropriate for workplace.stackexchange.com

Is the problem just one of the job market or have you lost interest?

@Buffy The job market looks dismal for my field. Just couple of job openings a month, with very specific requirements and experience, Also, the struggle of getting academic funding for my area of research seems soul-crunching. I have seen established tenured researchers struggling. Together, I am slowly losing interest, self-confidence and composure.

What are you trying to achieve?

Life may not allow for a redo, but it definitely allows for changes of direction when you find your previous plan is not working. You have not committed career suicide. At the very worst, you have spent a few years on something that interested you, without also advancing your career other than by learning how to do research, write papers etc. Let yourself mourn for the career you wanted, but then start looking forward to the rest of your life. The postdoc gives you some time to work out what to do next, and shift in the direction you choose.
There are three sets of issues you need to consider:

Your own likes and dislikes. Even if your first choice field is a dead end, you are likely to do better at something you somewhat enjoy, and avoid anything you hate unless the alternative is homelessness and starvation.
Your skills, assets, and resources. For example, even a bachelor's degree is a significant asset, and you have a PhD. You have the ability to learn, which will be invaluable if you decide to change fields. To get a PhD, you have completed a non-trivial project and written a dissertation. You have well above average writing skill and focus, and can prove it to a potential employer. I can only mention generalities. You should be able to list specific skills.
Available work. There seems to be a shortage of academic work in your current field. In that case, you need to either change fields, or switch to industry, or both. Deciding which is best depends on your field, skills, and what work is available where.

Your school may have career councilors. They will be primarily concerned with helping students, but may be available to postdocs. Talking all this over with someone could help.

I'll give this a different focus than the answer of Patricia Shanahan.
Sometimes the job market in a field is just terrible as it was for me when I finished my doctorate (long ago). There were no jobs for mathematicians and others in my graduating group were working in gas stations, and such. Such times are bad, but they are also cyclic and things may turn around in a few years.
But your degree gives you other opportunities, not just focused on research. In particular, if you are in the US and can teach, then a career in a liberal arts college can be very fine. The work will be mostly teaching, but there are research opportunities. Research that can involve undergraduates is especially valued in good colleges. If you are in a metropolitan area, there are probably lots of potential collaborators at neighboring schools. You can even make a career at a community college, teaching lower level courses, but also getting students on their way in education.
I spent a lot of years in a college with only a very local reputation. But a lot of students were able to reach beyond their origins and do some good things. I was also able to leave that behind for places with a wider reputation.
But then, as I saw myself as a young person, only academia would do for me. So I stuck to it and made the best of each opportunity that came along.

"things may turn around in a few years."  This is mostly a lie.  And a widespread one.

In many fields there is very intense competition for jobs at liberal arts colleges or even very low paying community colleges.  This answer is way out of touch with reality.

@AnonymousPhysicist you seem to have very little perspective. I've witnessed the job market ups and downs several times over my career.


text:
DAAD funding for stay abroad for PhD students and postdocs: is it added to the regular TV-L salary?
There are several funding options from the German DAAD for PhD students and Postdoc working in German universities to visit other countries:

Research grants for doctoral candidates
Research grants for young researchers with a doctorate (postdoc program) - short grants
PRIME Postdoctoral Researchers International Mobility Experience

Question: Are these funds added to the regular TV-L salary that the postdocs or PhD students receive from their own university? Or do they replace such salary for the duration of the stay abroad?

How much is it (compared to, say, 50% TVL)? That might give a hint.

The answer is found in https://www.daad.de/de/im-ausland-studieren-forschen-lehren/stipendien-finanzierung/wichtige-hinweise-zu-daad-stipendien/, Section E, Point 4:

If you are receiving a salary as a PhD student, the "domestic part" of the stipend - currently 850 EUR - is substracted from your DAAD stipend.

Note that there is a direct link to that site (explicitly referring to Section E, for precisely such kind of questions you ask) from the 1st page you link to.


text:
How to move from a physics background to a career in biology research
I have a bachelor's degree in physics and I am finishing my master's degree in applied physics, in the field of biophysics. So, in particular, I study methods typical of physics to investigate biological issues.
I have to choose the argument of my master's thesis and only now I realize that my interests and, perhaps, also my skills, are more oriented towards interpreting biological results and their implications in biology itself rather than studying and improving methods for obtaining them.
My academic career was not really brilliant: I did not graduate with full marks in my bachelor's degree and now I am taking more than 3 years to get my master's degree in applied physics.  But my dream still remains becoming a researcher: I always love studying and the idea of leaving studies makes me very unhappy. Thus I still really would like to obtain a PhD but in a research area in which I could be really useful in the future.
Is there a way of doing a PhD and at the same time studying a new field? Like a PhD in computational biology and at the same time taking a biology bachelor's and master's degree?
I saw that also Gary Stormo moved from physics to biology and received his PhD when he was already 31 years old. However, after this master's degree I can not go on only studying but I have to also work and the ideal plan would be to do a job that allows me to apply my knowledge acquired in my physics university and at the same time go on studying biology.
I am from Italy and I would like to remain here in all this. But I ask you if you know, in general, what I could do in this situation.

It is very common to change your field during PhD. I am not familiar with the Italian situation, but in other countries you generally can do it straightforward, especially if you are already well educated in e.g. biophysics. Find potential supervisors, find ine who appreciate and can use your skills and she/he will help you with the transition.

I don't see any problem with this. I think many biology labs would be very happy to employ a PhD student with an MSc in applied physics.

@gnometorule yes I imagined that it was not feasible to attend both PhD and an other university simultaneously and thank you for the suggestion. Do you mean that if I work as a technician first I could acquire the enough knowledges to apply for a PhD in biology? But I would like to deep in it so find a way to do also university in biology. Anyway you suggest that I don't have to mention that my plan is to attend university in biology when I apply for a PhD (that is reasonable) but, as Greg suggests, I should mention this to my master thesis supervisor, for example, so that he can help me ?

thank you @Louic for the encouragement .

I think what @Greg was saying is that if you find a supervisor for a masters (or Ph.D.) in biology (or a sub field of it) who sees the value you bring to the table with your physics background, then they’ll teach you what you need to know. It won’t be easy, but I agree with that. As to going technician -> Ph.D., I know several such cases at good U.S. schools; however, they tend to have a strong cs background too, so you’d have to make sure that your coding is up to par as well and ideally know some ML or statistics or such.

ok thank you very much !

Don't take is as a spam, but maybe check this program: it recruits a substantial number of physics students: https://mattertolife.maxplanckschools.org/application.
Disclaimer: I'm a student in the above program and coming from Physics and Mathematics (double-major) background..

Thank you @Our for this information .

What sort of internships have you explored?

My answer would be, don't underestimate how much you learn through doing and interacting during a PhD.
There are many interdisciplinary groups offering PhD projects for people with a physics degree and little or no biological knowledge, but within which you'll be strongly exposed to some biology questions. That won't make a biologist of you, but biology really requires many biophysicists who are able to frame a biology question in physical terms, and make use of physics and mathematics to solve these. Biology departments around the world also hire as principal investigators people who have a physics degree and have not become biologists, although they have learned a lot of biology on a specific system.
So I believe a PhD in an interdisciplinary group, possibly located in a biology department, could be suitable for you and could offer you the opportunity to face research challenges which are very biological, for which physical knowledge is needed but not the development of new physical concepts.

Thank you for your answer . Yes I saw this aspect also doing some projects in my master degree... I learned a lot of biology but I felt so frustrated that I had to limit in using maths, statistics, programs or softwares to reach some results and then stop because I do not have enough knowledges to interpret them deeply but I just have to give "hints" to biologists or medical doctors as sometimes a professor told about our role.

I believe this will be the case if you are in a physics group collaborating with a biology/clinical research group. If you are within an interdisciplinary group, then the PI will have had to take care themselves of this question and either acquire the necessary knowledge or hire group members who have this knowledge.

First (the bad news): Gary Stormo lived in a very different world. At the time science was working in a much more compartmental way: For example, a physicist solving partial differential equations (via numerical models) in biology, if the numerical model was succesful, it would have been hugely succesful. And nowadays the same numerical model or the results would be common knowledge of a biologist.
Second (the good news):
"my skills are more oriented towards interpreting biological results and their implications in biology itself rather than studying and improving methods for obtaining them."
There you are, you can either go down the statistics way (as a physicist your rudimental knowledge would be a good starting point) or the modeling way (as a physicist your rudimental knowledge would be a good starting point). Both ways, since you would like to interpret data, instead of producing machinery to produce them, it would be good to push up your informatics skills: learn R (maybe I am outdated already?), play around with opensource code used in biology.
Final note: There are companies and research institute looking for qualified people, and those companies are doing very interesting research, so do not completely discard looking for a job instead of following the PhD path.

Thank you for the answer. 1. I know this changing in the science but my willing is not solving partial differential equations (otherwise I wouldn't have felt unhappy). 2. ok yeah I know R and Python but without biological knowledges I can't go very far in interpretation :) anyway with the final note do you suggest to look for a job in a company that does research instead of PhD and this would allow me also to go on studying biology in university ?

1/2 Well, if you work in a company you have at least a job (we do not live out of thin air) and exposure to topics relevant to the "biology" subject (not necessarily the topics you would like to research as PhD, but they would be still relevant).
A decent paid job (and with decent working conditions) would allow you to enjoy your free time. Then you can occupy your freetime by studying biology.

2/2 Being a pessimist, a PhD in biology would leave you the same freetime (i.e. zero), because you would have the PhD job, plus you'd be almost required to spend your freetime working on your PhD (it is not a certainty, but it is statistically true that most of the PhDs students work way more than 40h a week). The big difference with the industry is that your PhD depends (somehow, it is absolutely not linear nor univoque ) on how much of the freetime you spend on it, while working in the industry your job depends on what you do in the 40h a week, how you spend your freetime is up to you.

I understand, thank you very much.

My (obviously limited) personal experience shows it's not always super common knowledge. Sure, the lowest-hanging fruits have been picked up but there's more at the level trivial for a competent physicist but still out of reach for a classically trained biologist. They get picked up quickly though now so it's only going to het harder from now on - but it's still a great time for interdisciplinary research!

Do you know if there is a way of doing a PhD and at the same time studying a new field ? Like a PhD in computational biology and at the same time taking a biology bachelor and master degree ?

I don't see why you would need to do a Biology BSc/MSc if you already have physics degrees. I am a biologist and have had many colleagues doing their PhDs in fields different than their degrees. In a Neuroscience lab, we had people whose bachelor's/master's degrees were in Biochemistry, Physics, Informatics, Biology, Molecular Medicine, etc.). It's quite common to change fields for your PhD and most labs are quite happy about the interdisciplinary collaboration that comes from having people with different backgrounds working together. If you wanted to learn more about a specific area of biology, you could probably take a free course at the university you're doing your PhD in (at least in the universities I've been in, you could ask professors to sit in lectures and it wasn't an issue as long as you didn't need the credits).

Thank you @LDB_2016 for your answer but... I imagine that physicists in a neuroscience lab apply their physics university knowledges so I think, for example, they decide the parameters needed to acquire MR images, they use/create algorithms to investigate this images or they simulate interactions between different parts of the brain with complex networks algorithms implementing them with a programming code etc... The point is that I just realized that I am not really interested in all this but I am more interested in interpreting the results that all these methods will bring

in order to know biological implications .

Oh no, these were wet labs doing basic research. The people with a physics background were doing the same/very similar type of research and work as the biologists. While doing a PhD, you design the experiments, execute them and analyze them/interpret the results. It's entirely possible to learn to interpret the results from a biological perspective during your PhD. As I said, some classes are open to PhD students and your colleagues are also a great resource. Plus, you could always pick up a textbook for yourself. My point is only that you don't need a biology degree for this

Wow! I did not know this thank you very much... @LDB_2016

Francis Crick did just this. Find a congenial environment. To do this, spend some time reading journals to find articles and scientists who do work that interests you. If they are at universities, apply. This is one of the rare cases where I would recommend contacting someone and meeting them to assess your past education and what you might need. You might only need a little bit of biology, possibly through informal mechanisms rather than courses.

I think examples of famous people are not very useful for a question like this, and more broadly, historical examples are not very useful for the present date.

I disagree. I cited one person but have heard of others. I have been told more than once that  many geneticists started as physical chemists. This kind of transition reflects the expectations that the different sciences have of undergraduates regarding quantitative methods and probability.

I don't disagree that this is a very possible transition, just that famous people aren't good representatives. It's much more useful to talk about how prevalent this is among students/researchers today, like LDB mentions that it's not uncommon for neuroscience PhD grad students today to have bachelors or masters degrees outside biology.

Thank you @DavidSmith for the answer and I like a lot historical examples of famous people :) so do you suggest to contact some professor/researcher in biology/medicine and to explain my situation ?

Thank you @BryanKrause for your observation even though I think that historical examples may be useful in order to have an idea of the attitude that one should have to do the transition... I mean: I agree that today many things are different in science with respect to the Francis Crick's scientific world but the "spirit" of a physicist who decides to study biology is the same. Then of course examples of present dates would be more useful from a practicle point of view so I thank you again for the idea of neuroscience labs.

@Manuela. You can contact people in the field. Some will be helpful and many will brush you off. Go prepared by reading research articles and understanding what biologists do. Clarify in your own mind how your knowledge would fit in.


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Suggestions about possible ways to improve my position about PhD applications due to my own misstep
My post is related to a previous question but this time I think it is more clear for people to answer.
So I finished an integrated Masters with very good grades and a strong thesis in field A.
And then due to covid I made a strange choice and moved to a very similar Masters and due to personal problems I did average in the grades( that for the 2nd university is considered more than sufficient) and averagish thesis in a field B still relevant but very different on the research workload and techniques.
Unfortunately while doing B my daily supervisor gave me a direction without any elabboration and plan. The more I tried I didn't find joy doing it, his help was bad and minimal. He also struggled with his own research field. I also had personal problems due to anxiety and other issues and struggled immensly. Generally the supervisor above remained very unsatisfied with me and  this already affected a phd application fo mine where I included him, since he also agreed. I was one of the 2 last candidates.
I found out throught my 2nd experience ending how to finally stand on my feet and figured I should have never left area A since it's the only one I would like to do a PhD - I am keen to continue in that only.
I understand that in academia that nobody cares about mental health and I am also no interest to try to defend myself and say I was anxious. I want to move forward and found 3 solutions:

Avoid including supervisor from field B and see which university accepts me with references mainly from uni A - since the professors there are scientificly more relevant to A.

Including him and putting him last and try to defend in my cover letter and ( maybe - although unprobable that I will reach) interviews how much actually he observed me ( because he didn't really much see me much on action) and question the differenec in the two fields.
I will also include that I found that I was not interested in field B and learned how to do my work  in that field and learned some things - but found no interest to proceed further. Although A in the meantime became more interesting to me.

Go to industry and R&D , gain experience and ask  references from there when I will feel ready to try again?

I am contemplaiting in initially doing 1 and 2 in different applications and have 3 as my main target.
Any suggestions , considerations , comments would be really helpful!

I've made some bad choices, but made it in the end and am now mid career as a professor. I won't go into any detail, but just want to reiterate the answer below, that, if you are sufficiently young, then you have time to learn and recover.

thank you! yes I am still young enough I hope!

Let me also add that what has helped me was really reconditioning my mindset/mentality. Beating back the tendencies to make poor decisions and to become more professional in my behavior and less reactive. Also lowering the effect of my own sensitivity and self-judgement on my mindset. If there is a serious mental health concern, professional help could be appropriate. Something like mindfulness meditation could be helpful to these ends as well. Give it some time and deep effort/introspection/self-reflection. I hope within the next decade to see you update this post with a story of success!

very different on the research workload and techniques.

Ignore the workload, focus on the techniques: you learned how they do thing in field B. Whether you can build on that, you will do that again, you will integrate the strong point from there into A, whether you will despise any person in field B jsut because field B, it is up to you.
1 and 3 are not mutually exclusive. Get back in touch with advisor from thesis A, you may describe very briefly your goals (pursue a research career, i.e. a PhD in field A). Since we all need money to survive, try to get a job in the field.
2 is very convoluted. Why should you try to get a reference letter that put you in the uncomfortable position of defending yourself against it? A reference letter should be at best something that helps you, at worst something that fullfill a bureaucratic formality, not a disadvantage.
I would personally consider field B a closed door, there are way less emotional costs in counting it as "past experience" and not doing any effort in keeping the contact there. Your mileage may vary.
You are what you are, but do not keep on bringing the burden of "strange" choices. You do not need to justify them, nor to judge yourself for them, the advantage of being young is that you can do plenty of "wrong" choices and you can learn and recover from any of them.

Thank you for your answer! I will take into consideration your advice. Especially the last part, it is something really important for me.


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What does competitiveness of a journal mean?
I was looking at metrics on Letpub for few journals. For competitiveness, few journals had "very difficult", few had "86%" while some other had "2%". What does the percentages represent? Is it similar to acceptance rate?
Example:
https://www.letpub.com/index.php?journalid=765&page=journalapp&view=detail

From that page: "All review process metrics, such as acceptance rate and review speed, are limited to our user-submitted manuscripts. As such they may not reflect the journals' exact competitiveness or speed."

Based on the percentages, I would guess that "competitiveness" here means how many articles are accepted out of those that are submitted. Elsevier sees a much lower acceptance percentage, which makes sense, because the people who submit the worst papers that get desk rejected don't likely report what happened to the database. In the same way Elsevier reports a much shorter average review duration compared to the user-reported ones.


text:
My postdoc advisor just now said she cannot support me after 6 months. What should I do?
After graduating in February, I was waiting for my work permit to start my one-year postdoc position. Finally, after 2 months delay (due to COVID-19), I have got my permit today and now I can start the paperwork to have my position finalized. However, now my postdoc advisor informed me that there's a change in the financial situation due to an industrial funding partner retracting their contribution and I can be supported for only 6 months. So, now I am clueless on what to do about this.
What should I do? I am going to start applying to positions again from next week. Any other advice for me?

This depends on your personal situation, such as relocation costs.

I would start the 6 months post-doc position and look for other positions in the meantime. Also, there is a chance that your contract might get extended within those 6 months as other funding opportunities may become available.

Given that your contract wasn't finalized, there probably isn't much you can do.
But there are a couple of options, all risky. You could ask the PI if there is any chance that additional funding could happen to at least complete a year. The answer might be maybe and you could decide to take a risk and do the short postdoc and hope for more. In fact, you could ask to be first in line for additional funding. You might actually be able to help secure funding as part of your work.
You could also, just drop out of the position and search for something better, provided that you have some way to make that work.
But looking for another position immediately is certainly a smart thing to do.

Yes, I am searching for more positions. And the PI has told me that if the funding situation changes, she will extend the contract.


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Quit PhD two years ago, now I want to go back?
I quit my Ph.D. two years ago because of multiple reasons but largely due to my own naiveness over deciding to enroll for a Ph.D. I decided to do a Ph.D. without knowing anything about it. I wasn't prepared at all. I wrongly chose a lab that has a very poor vision for any scientific advancement. I foolishly chose a supervisor who had no idea what's going on in his lab. Once I understood this, I also became aware of my own weakness that has resulted in not getting me an ideal lab. This realization happened very lately and until now I had already developed a strong vision for my research project and my future career. And according to my plan, it wasn't that lab or supervisor who was going to help me to reach my goal. In academia, everything is connected, so if I wasn't going to be the best version of myself in Ph.D., the chances of finding a better opportunity after my Ph.D. was very less. So I decided to quit my Ph.D. and start it all over again; only this time knowing everything about a research career and how to excel in it. I wanted to become the best and for that, I had to work on myself first. So, a six month gap period was planned after leaving my Ph.D. But this gap time became much longer (because of some unfortunate circumstances); almost two years now and I have started feeling like a failure. I really want to go back and do some quality research. What is the best way to do it?
P.S. I am from India and I am talking in terms of the Indian research institute.

What is wrong with just making application?


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Going back to academia after quitting my Ph.D. and taking a year off?
I am a Ph.D. dropout with a one year of career gap. I want to return to academia, but now  I have realized that it was perhaps the biggest mistake to take a gap after quitting my Ph.D. The purpose of taking a gap was to work on my communication skills and get a  new perspective on my work and my career in science. This could have been done within a period of 2-3 months but it became one year long because of my own recklessness. I allowed myself to distract from my goal and I started working on my hobby i.e. Painting. I lost myself there and completely lost track of my time. I was really enjoying everything about this new venture. I took it as a challenge to become better at my skills in painting. Eventually, I became the best in my group and got lots of appreciation. But then, I lost my interest while realizing that there was no further challenge and all there was left is to work and work while crafting your art which was never going to be perfect. It made me realize that what I actually love is to take the new challenges and work on myself. To be an artist was never a career option for me, all I wanted was to learn the skills. That's it!
While counting my achievement in science, I  realized that it was an irresponsible thing to take a gap in doing something that has nothing to do with science. Earlier I had a scholarship and a very competitive mind that has led me to get a Ph.D. position in one of the best labs in the country. Now I don't have the scholarship. I want to go back to my world of research where I was accelerating exponentially. I want to tackle the challenges of science with a new perspective and better skills. I want to be productive more than earlier and ready to take all the tough challenges.
But I feel embarrassed about my past mistake. Because of this, I come across as someone who is not sincere about her career. But I can't help it because the truth is that I did behave insincerely by losing track of my time.  I should have been conscious enough to realize the consequences. Now, what do I do? The past has gone and the vision of the present is crying for a better future. How do I make things better like before?

This is more of a complaint than a question.

First of all, please appreciate your self.. I assume you are from India.. As you might be aware, it is very common in this country for some one to take a break in their academic career and come back with a bang...  Welcome to academia...

This could have been done within a period of 2-3 months but it became
  one year long because of my own recklessness.

I did not notice any "recklessness" in your post -- instead, it sounds like you have been very proactive in exploring for yourself what you want to do in life. Taking a year off may have been the best decision a year ago. Now you know more than you did then; don't fault yourself for what you did not know.

I started working on my hobby i.e. Painting.
  I lost myself there and completely lost track of my time. I was really
  enjoying everything about this new venture.

Your enjoyment is important, too; not just your career. It sounds amazing to take a year off and work on a hobby. In fact, many career academics wish they could have done this when they were younger, because it is much harder to find time for such things the more work and research you get involved in. Remember that you did enjoy this, and enjoyment can be rare and valuable.

But then, I lost my
  interest...It made me realize that what I actually
  love is to take the new challenges and work on myself. To be an artist
  was never a career option for me, all I wanted was to learn the
  skills.

Try to think of it as a positive realization, not a negative one. Many people spend a lot of time (decades even) before they realize they want to do something different. Learning about what you want to do helps you see the future more clearly.

While counting my achievement in science, I realized that it was an irresponsible thing to take a gap in doing something that has nothing to do with science.

Why is it irresponsible? You may have given up your scholarship, but you learned a lot about yourself in the process. I am not sure you could have done this any other way.

I want to go back to my world of
  research where I was accelerating exponentially.

You can do this. Don't give up on yourself and what you really want.

But I feel embarrassed about my past mistake.

Why are you embarrassed? Was it truly a mistake if you learned a lot both about your hobby and about yourself?

I come across as someone who is not sincere about her career.

You do not come across that way to me, at least. However, you do seem to be very upset and beat up on yourself.

Now, what do I do? The past has gone and the vision of the present is crying for a better future. How do I make things better like before?

The first step is to understand that you have a lot to be proud of. You may not have the scholarship now, but you earned it before, and you are still the same person. You are highly capable and have spent a year progressing in a different hobby, which you are also capable in.
The second step is to get advice from academics who know you better about what is the best past forward to get back into good positions. It may be that you can simply apply again; I don't think taking a year off is necessarily a problem. Or it may be that it would be better to get some more experience first, such as applying for some industry experience, or getting a masters' degree.

I truly appreciate the time and effort you have put into while reading each and every paragraph and I sincerely thank you for making things simple for me.


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How do I tell my supervisor that I don't understand something which is probably very basic
I am currently a first-year Ph.D. student in computer science in Europe. I have published some papers in the top-venue conferences.
Recently, we are looking into a new field that requires strong mathematical background, but unfortunately, my math skills are not that steady. Whenever I encounter something I don't understand, I am always confused about whether I should have learned it in the basic courses and don't know how to catch up with it. I am also worried that my supervisor would think me less qualified if I admit that I am not sure about something.
I am wondering how people manage this. Should I just be strait-forward with my supervisor? What would he think of me and what would he probably do?
--- Edit ---
Thanks for all of your replies and suggestions. I especially appreciate the answers/comments from the perspective of supervisors since I really have no idea how my supervisor would react to it. I am probably overthinking and feeling less confident in this new field. It is also good to know that I am not the only one who faces this problem.
After all, I think I would first try to find some references and teach myself first though it may be very challenging to me since I am sure what courses/subjects would cover the specific techniques I need for my research. If it still doesn't work out, I would show what I have tried during the past week and see if my supervisor could point me to any further resources.

As a bit of a confidence boost: You state that you have puplished some (i.e. >1) papers in top-venue conferences. That is a lot for a first-year PhD student. Don't be afraid of minor problems like missing math skills.

haha, one of my supervisors favourite comments was "As you remember from undergraduate...." in a tone that implied he was well aware I had forgotten it, or never properly understood it in the first place. We got on fine overall though, I think it's normal to mess up some basic stuff.

Reminded me of this interview: https://www.youtube.com/watch?v=u3Pq9Okpycc

I am wondering how people manage this. Should I just be strait-forward to my supervisor? What would he think of me?

Yes, you should be straight-forward with your supervisor. No good will come out of pretending you understand something, or know how to do something, when you really don't. Even if they "think less" of you, they will find out eventually, and this way you have at least done the right thing and alerted them of the problem as soon as you noticed it.

What would he probably do?

Well, that depends on the supervisor, their expectations, and what kind of knowledge we are talking about. My expectation is that your supervisor will recommend you some resources to study, and/or teach you the basics themselves, and/or ask somebody else in the lab (for example a postdoc) to teach you the basics. Maybe they also decide that you are after all not the right person to explore this new field with, and recommend you to change your research direction to something that's more aligned with your prior knowledge.
Independently of how they react, it's better than stumbling forward without knowing what you are doing. That's how failed PhDs start.

I think its very unlikely a supervisor would "decide that you are after all not the right person to explore this new field with, and recommend you to change your research direction to something that's more aligned with your prior knowledge".

I second the advice to be straight-forward, but I think you're overthinking this. A PhD supervisor is unlikely to regret hiring a PhD student just because the student asked them a math question. In fact, I know many PhD supervisors who often say that their students don't ask enough questions.

Yeah, sure, but OP also said that they have published before and they and their advisor are now considering exploring an apparently rather different field. If I'm an advisor I could see myself saying "ok, if field A is super formal and you don't feel comfortable with that, let's continue working in a different direction" (and then exploring field A with a different student). I wasn't suggesting that the advisor would kick OP out, that's indeed rather unlikely.

@IanSudbery I have seen this exact situation happen several times, with different advisors. How likely it is to happen might depend on your field. In software engineering, there's a broad variety of methodologies (empirical, formal, constructive) that fall under the same broader umbrella.

Never forget one universal fact: Nobody was born already knowing all this stuff. Everybody has to learn it. Whether you learn some particular thing at age 16, 26, or 96 doesn't really matter.

@xLeitix - sorry, I misunderstood, I was assuming you were suggesting the supervisor might kick them out.

I once asked my supervisor "When will I know enough to stop having to look these things up?" and the simple response was "Never!". Everyone (even supervisors!) has to look things up, everyone has to revise things at some point. There is no shame in this. It might be that you ask your supervisor only to find that he/she promptly goes and looks it up.
Your supervisor will probably not think badly of you for some maths naivety. You lack knowledge, but you have enough self-awareness (and knowledge) to identify this fact. You now need to fill the gap in your knowledge. You can either do this by asking your supervisor, as you've suggested, or you can try to do it yourself first.
Don't worry about whether or not you should have already learned this. Maybe it was covered briefly but you didn't know you'd need it in future so you've forgotten it, maybe you didn't even know it existed in the first place. No one can blame you for that.
Figure out if you can learn it yourself. What do you already know? What resources do you have? What do you need to know to accomplish the task. Your supervisor is one resource but are they the best one for this purpose? It might be that they can point you towards some resources, but maybe you can find these yourself if you try. One way you might annoy your supervisor is by using them as your first resource for every single thing. Try to educate yourself first so that you know which questions to ask when/if you do ask your supervisor. Also, consider what kind of resources you need: do you need a personal one-on-one tutor or an online course or just a series of tutorial videos? Does your university offer sessions with a maths tutor or will it have to be your supervisor?

If you are going to talk to the supervisor, I imagine it would help to say something like "I looked at [resource X] and [resource Y], but they weren't very helpful because [Z]." Then your supervisor can give an answer like "[X] is terrible, don't use it!" or "Here's how to overcome [Z]."

Relax. There is a lot of truth in the old joke: "The student has to know it. The post-doc has to know where to look it up. The professor has to know where the post-doc is."

Just do it if you cannot figure it out yourself! I'm so much happier when this conversation happens as it firms something that needs to be firmed in the foundations for my student!
The worst thing is that something basic ends up continually being an issue and I don't know how to help the student and something lags for months. Nip it in the bud immediately and directly. That really makes projects and research actually speed up from this issue rather than slow down!