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Failed to Apply for a Suspension of Studies - Feel Like Quitting Now

First thing I would do is contact your supervisor. It might not be a big deal. Explain the mistake and see where you stand.
If no one has said it, it's likely they haven't noticed it- have you missed a reporting period etc?
You will get great advice on this forums-however in this instance the best thing to do is contact your supervisor asap- any see where you go from there.

How do you tell if your PhD supervisor is sexually harassing you?

What he is doing is not okay-I think you need to address that with him- I wouldn't mention it to others in the lab- that has rumours start and could have a negative impact on you.
I agree with Abababa- next time pull away but also say that you are not comfortable with that- make in very clear. If he hasn't be aware of what he's doing- he would be shocked!
My other suggestion is to arrange a meeting with other around- can he come to the lab -don't be in his office with him- try a canteen etc.
Unfortunately at the end of the day, you're a student and he is your boss- if you make a formal complaint- it might not end well for you.

Corrsponding Author Question

I agree with Jamie, It shouldn't be an issue, in fact in all my paper form my PhD my PI is the corresponding author.
If you worried about your thesis you can always but the contribution at the start of the chapter, indicating what work each person did (My examiners requested this).

Is this Normal?

I have heard of a project proposal and writing samples being request but after an interview, but. It can be so competitive so maybe that is the case. I would be wary of giving someone a full literature review though, there not something you write overnight and can change greatly during a PhD project.
I do know it more common to ask post-docs to supply those things before interviews.

Selecting journals for future publications

The first thing I would do it look at where you PI and other colleagues are publishing, that will be a great start. The read the aims and scope of those journals, will they work? Secondly, what journal are you getting your information from or a reading form a lot, also a great place to start. If there is a project proposal, that might have mentioned some. I would also look at people in your field, who attend the same conferences etc. where are they publish or have published.
It can be hard to choose a place, and not every journal will suit every article, but if you don't submit it you'll never know. I usually make a list of 3-5 journal per article and ranked them in other of my preferences, from there I then ask the co-authors their thoughts, once we have an order and the articles ready we submit and hope it gets accepted, if not we then have a list of backups to go with. Some journals are also quite good at the given suggestion in their publishing house if it doesn't suit there's.
You could also send an email to editors, with a brief outline of the article, asking if it something they would consider publishing-some of the top journals (nature, trends etc) required you to do this first.

Different area of post-doc after phd possible? / Drop out of PhD for Mres or not?

Of course, doing your PhD in the same field as your postdoc makes you stronger candidates compare to someone changing fields... but it comes down to how well you see your self to PIs.
My PhD was in biological and chemical wastewater treatment (background as a scientist)- For my post doc, I switched to biofuels/biogas production (lab full of engineers). Slightly different area but the underlying theory, skills and lab work are very similar, so it was an easy switch, but require a lot of reading in the first few months. It's doable but you need to show a big interested in the area your changing to, and able to highlight the skills you can bring over.

Part - time Mres along side PhD.

Look into the requirements at your chosen uni- I know from a friend doing a Mres, that she has to be completely finished and off the master register in our uni before she could join her now uni for a PhD programme.
Personally, I think they might frown upon it, it could be seen as you not be really interested in your current PhD. In terms of them not knowing, if the Mres is funded who are you using as a reference? I started out on the Mres and transfer to PhD in year 2- they work the same and require the same commitment.

Postdoc responsibilities

I don't think it would be a conflict, but wouldn't discuss your researcher if you were at a different uni doing it. If your only looking for short term contacts and it won't take away from your research I wouldn't worry about it.

Formatting thesis including published articles

First I would double-check what the mean my maintaining format- for my uni that just meant keeping the same heading and information etc
So I added in the word document that I would have sent to the journal for review -I didn't put in with two columns etc- I did change the referencing to match and on the title page foe reach chapter I wrote this paper title XXXX was published in XXX and gave the DOI and author list plus contributions.

The other option would be to save up as far as the first paper as a pdf, your pdf paper, then the next part as a pdf and merge all pdfs together or alternative leave blank pages for the pdf in word, print your thesis- on the pages for the pdf print the pdf on these pages, but the document back together and scan the completed version.

Postdoc responsibilities

First thing I would say is to talk to your PI and create and professional development plan- what skills do you want to achieve and how do you get there? Can you ask for a mentor (Not related to your project or PI) that can help with advising on how to reach your goal etc.

After my PhD I took up a post doc (two-year post- left after year 1) in a different uni with an international PI who well knows and respected in my field. I was so excited to start work with him and soon released the post wasn't what I expected- there was no opportunity for teaching, I was given PhD students to mentor( But no acknowledgements for this on paper etc). After coming from uni with encourages PhD student to get involved in teaching labs I was so discouraged.
I recently started back as a post-doc(4-year contract ), where I did my PhD and straight away both my PI and head of the dept have asked for a personal development plan, they have even found me a mentor form a different college to talk to and help keep my goals in line and support my professional development.
My biggest goal was teaching experience, but with by contract 100% research, it would be hard. We have settled on me taking final year project next Sept. I have been put forward and accepted to begin a master in teaching and learning (Thankfully the uni is covering the cost). And come next Jan I will be given 1 lab class a week during working hours and have been an offer and teaching role in our evening course dept which is 4hours over two nights. I will be paid for the evening course but not the lab class, which doesn't bother me as it a good experience.

I would, however, check your contract for T&C, mind said no other roles unless approval is given my PI, and head of dept etc.

Combining thesis into one document

I would have started working from a full doc in the last 3 months of my thesis, while I was waiting on final comments from my PI. My final doc was 430 pages and 6.5MB. I never had an issue working from it (use a laptop that was given to be on day 1 on my PhD, it was old and sluggish).
I found to work around the document etc, I needed to have heading and subheading in the table of contents, in order to prevent scrolling.
From experiences, formatting takes longer than you think.. so I would start now. I would also recommend conversion a word doc to PhD every so often to see how it will look when printed, I found blank pages, large spaces etc by doing this

Covid Contingency Plan

I agree with rewt. Try plan out your expeirments as much as possible-For each method what material do you need. For examples I am starting a new batch of trials in 3 weeks ( if i am allowed back in the lab) and I have pre-made data sheets for excell,made a list of material needs like shaken water baths etc and check with other lab mates there requirments, to make sure I have what I need and wont be set back due to equiment. Likewise for regents etc find out what you need what there and order stuff thtas missing. Try plan stuff for the gaps if you have long wait times.

Depending on you lab rota it might be worth teaming up with some people . For example there are a few of us running similar expeirments and will have access on different days- they will monitor my trials when im not there and vise versa. Equally for prep work were planning to make similar items in batches to share out. I also wouldnt plan long experiments if you can help it that way if you have to shut down you wont have lost months of data.

The work I am doing requires public input- at the moment I am arranging as many video calls as possible and sending the a list of question/things i want to dicuss pre-call, thatway they will equally be prepared they can equally be prepared.
In terms of stuff you could do outside the lab - review paper, moddeling, get you head around any equations that you might be needing.
Read as much as possible- get on top of references- attend online training events- talk wiht your boss and see if they have any old data that you could be working with.

Looking into doing a Masters in Ireland and have questions

1. There is one particular uni better or worst at accommodating difficulties, it all personal experience.
2. In terms of staying in Ireland after grad, look at courses that offer work placement etc. In terms of during, I cant really say but I'd imagine there all the same.
3.SUSI grant are means tested and it doesn't change much from year to year. Look at there website the info is there, they also have a checker. But be careful, as far as I am aware you have to live in Ireland for 3 out of the last 5 years to be eligible. Also, for postgrads it only fees that are covered by this. I could however be wrong, its a while since I would have looked at this system.
4. I dont know of any company that offers advice of help with this.
5. As far as I know, you would have to register as a patient with a GP over here to get scripts etc.

Best bet is to email the college about the course your interested in and get there advice. Also bare in mind a lot of taught course are online now !

Postdoctoral Fellowship

That's a hard one. What are the funder guidelines on it? I know some funder won't grant funding to do a post-doc in the same institute as you PhD, unless its a really niche area.
When I was applying for funding I used people who wouldn't be mentoring me as recommenders- my mentors taught it would look better.

Changing subfields between postdoc - good or bad idea?

I don't know what the correct advice is.
However, My PhD was in wastewater treatment (using reators), after my PhD I work as a research microbiologst (undergrad and 3 chapter in my PhD related to this) for 6 months, before starting a post-doc (2 years but leaving after 1 for a job closer to home) in reactors for biofuel production (ethanol) and in a few weeks a start another post doc in alchol production for the food industry.
I haven't came across to much issues which crossing over fields, once the underlying skill set are the same. Hope that helps