VirtualCell

Just got offer from Havard BIG and waitlist for TRI-I/UCSD ?

Jean Fan (a recently-graduated hotshot PhD Bioinformatician) gave some really fantastic tips here: https://jef.works/blog/2018/02/26/phd-program-interview-and-application-tips-and-advice/
I asked a similar question to two senior postdocs in my lab yesterday, and they were more succinct. They said (1) have a 1-minute summary of your current and past research projects. It's hard to do, and doesn't actually reflect your potential to do well in grad school, but it makes you look well put-together, (2) have a quick summary of why you like that program, and (3) remember to relax and let your interviewer talk about themselves!
Good luck! You're going to do great!  

I got an invite to MIT CSB at exactly the same time too

That was me! I'm also not sure if all invites were sent, but I got an email yesterday at 6:59 PM for interviews on either February 7th or February 28th.
My friend's PI was on the committee and was complaining about how they had ~400 applications for ~6 spots. I'm really shocked and grateful that they sent me an interview--but I feel like, with that many applications, there has to be even more stochasticity than in most. 

Depends on the program. One program I applied to called a handful of people ahead of time so we could hold the interview date before official invites went out. Some trickle them over a few days, and others release them all on one day. I had another program that seemed to rely on the PIs contacting us first and then sending the invite right after.

That was me! I'm also not sure if all invites were sent, but I got an email yesterday at 6:59 PM for interviews on either February 7th or February 28th.
My friend's PI was on the committee and was complaining about how they had ~400 applications for ~6 spots. I'm really shocked and grateful that they sent me an interview--but I feel like, with that many applications, there has to be even more stochasticity than in most. 

I got interviews at BU and Chicago and they are supposed to start soon, so I'm pretty sure they are done sending out invites. You can always email the program to see if they are sending out more or plan to send out some a little later in February. Based on previous years I don't think they are sending out any more but every year is subjective to the applicant pool so possibly asking them is the only way to get a clear answer.

That was me! I'm also not sure if all invites were sent, but I got an email yesterday at 6:59 PM for interviews on either February 7th or February 28th.
My friend's PI was on the committee and was complaining about how they had ~400 applications for ~6 spots. I'm really shocked and grateful that they sent me an interview--but I feel like, with that many applications, there has to be even more stochasticity than in most. 

Lol thanks. More like recklessness than confidence? Tbh I was going to take a year or two off--I'm in Boston and there're lots of job opportunities in Bioinformatics here--but one of my undergrad advisors (who I trust a lot, in part because she's blunt/honest to the point that it sometimes comes off as rude) told me to apply to a few places year, at least to get practice. I took it seriously and hey--so far, so good. And I'll get to meet you at the BIG interviews! ? I'm so excited, it's going to be a blast.

@VirtualCell I looked at your list of schools and commend your confidence

Jean Fan (a recently-graduated hotshot PhD Bioinformatician) gave some really fantastic tips here: https://jef.works/blog/2018/02/26/phd-program-interview-and-application-tips-and-advice/
I asked a similar question to two senior postdocs in my lab yesterday, and they were more succinct. They said (1) have a 1-minute summary of your current and past research projects. It's hard to do, and doesn't actually reflect your potential to do well in grad school, but it makes you look well put-together, (2) have a quick summary of why you like that program, and (3) remember to relax and let your interviewer talk about themselves!
Good luck! You're going to do great!  

Unhelpful to ask for an informal chat before interviews.
I found it completely unnecessary to read papers for my interviews in advance. I started off doing them, but the papers never came up. You should have an idea of what they do, but focus on knowing how to talk about your own research. Also know why you want a PhD and why that program is a good fit for you. They are unlikely to test your knowledge of their science, and more likely to test your knowledge of your own science.
You also won't be expected to come in ready to do their research. You're expected to show interest and intellectual ability, they'd teach you whatever technical skills necessary to perform research in their lab. It's school, after all.
I don't think any of my interviewers asked me about my strengths and weaknesses...
Your goal in the interview is to show them you're passionate and dedicated and KNOW you want to be there.

Just got an interview email from Harvard BBS!  I haven't gotten any other notifications yet.
Generic format, e.g.: 
> It is my great pleasure to invite you to visit the Harvard University Division of Medical Sciences Program in Biological and Biomedical Sciences (BBS). 
> Our Admissions Committee has selected you as an excellent candidate for entry into the BBS program.  The next step in our admissions process is an interview where you will meet individually with multiple BBS faculty members and receive a broad introduction to our program, our students and the Harvard Medical School environment. 
But I thought they wouldn't be sending anything out until January, so I was super pleasantly surprised! 

Just got an interview email from Harvard BBS!  I haven't gotten any other notifications yet.
Generic format, e.g.: 
> It is my great pleasure to invite you to visit the Harvard University Division of Medical Sciences Program in Biological and Biomedical Sciences (BBS). 
> Our Admissions Committee has selected you as an excellent candidate for entry into the BBS program.  The next step in our admissions process is an interview where you will meet individually with multiple BBS faculty members and receive a broad introduction to our program, our students and the Harvard Medical School environment. 
But I thought they wouldn't be sending anything out until January, so I was super pleasantly surprised! 

Just got an interview email from Harvard BBS!  I haven't gotten any other notifications yet.
Generic format, e.g.: 
> It is my great pleasure to invite you to visit the Harvard University Division of Medical Sciences Program in Biological and Biomedical Sciences (BBS). 
> Our Admissions Committee has selected you as an excellent candidate for entry into the BBS program.  The next step in our admissions process is an interview where you will meet individually with multiple BBS faculty members and receive a broad introduction to our program, our students and the Harvard Medical School environment. 
But I thought they wouldn't be sending anything out until January, so I was super pleasantly surprised! 

Just got an interview email from Harvard BBS!  I haven't gotten any other notifications yet.
Generic format, e.g.: 
> It is my great pleasure to invite you to visit the Harvard University Division of Medical Sciences Program in Biological and Biomedical Sciences (BBS). 
> Our Admissions Committee has selected you as an excellent candidate for entry into the BBS program.  The next step in our admissions process is an interview where you will meet individually with multiple BBS faculty members and receive a broad introduction to our program, our students and the Harvard Medical School environment. 
But I thought they wouldn't be sending anything out until January, so I was super pleasantly surprised! 

Undergrad Institution: Queen's University - Canada
Major(s): Life Science
Minor(s): Mathematics
Overall GPA(Undergrad): 3.83
Overall GPA (Masters):4.0
Type of Student: International

GRE Scores (revised/old version):
Q: 162
V: 162
W: 5.0

Research Experience: Two years summer lab positions in undergrad for reputable PIs. Two undergrad theses (bioinformatics, molecular genetics). Master's (molecular genetics) complete in May (expected). Visiting grad student in an HMS lab (synthetic biology).

Awards/Honors/Recognitions: Dean's list every year. Canadian Space Agency grant. A few smaller scholarships/awards. Two conference speakerships, one at an international conference (idk if this matters lol), one poster, one paper published in conference proceedings, one journal publication submitted.

Pertinent Activities or Jobs: I've TA'd three undergrad courses in molecular genetics / bioinformatics, Won a ntl. research competition for conducting MSc. work in 0G w/ the space agency.

Any Miscellaneous Accomplishments that Might Help: Lots of extracurriculars and volunteering experience

Special Bonus Points: I haven't been in my current position all that long so I might not ask because idk if it's appropriate, but my current supervisor is pretty well known so she would definitely help as a reference. I don't know, I think space is pretty cool and unique on an application, not a lot of people have flown with their theses in zero gravity, but maybe I'm a bit biased, some adcomms might definitely view space life science as a bit fringe even tho its totally cool!

Any Other Info That Shows Up On Your App and Might Matter: I guess I have a pretty broad skillset, bioinformatics, laboratory work, mechanical/electrical engineering... I had to built my thesis before I could use it to test genetics things! but I feel like a lot of people have diverse academic backgrounds and stuff.

Applying to Where: A few places in the States, I only really want to go down there if I get into a moonshot program so don't hate on my smaller sample size haha. Otherwise I'll tough it out at U of T and try to get a prof to let me do synthetic biology in their lab!
Harvard BBS
Harvard Systems Biology (dept. in which I'm working now)
MIT Biology
MIT Bioengineering
Stanford Bio
Stanford Bioengineering
University of Toronto (maybe MolGen, maybe CSB, idk)
My main question is really whether to include my GRE scores on applications where they are optional, like I know my scores aren't bad, but there are many applicants to the programs I selected with higher scores, will submitting a 5.0/162/162 help or hurt me? I would honestly be so appreciative of any opinions you may have!

If it interests you, I've done research in bioinformatics and my CV is here: https://drive.google.com/file/d/0Bx-Anz53UhD1ek9xd0dudVVpTzQ/view
In response to your questions:
1. I wouldn't put a separate line for each. 
2. Preprints are fine. Make sure you mention that it's a preprint, though.
3. You can definitely include Coursera work. Whether people take it a serious work, though, is a different story. 
4. I think you can definitely include those things. On my CV I've explained my science writing experience, even thuogh it's not directly related to my work as a researcher.
5. There's no page limit, but be as concise and succinct as possible. 

I hope it helps! I've found The Professor Is In by Karen Kelsky to be extremely helpful. She also runs a blog, which you can google and find a lot of free advice there. While she has experience as an R1 program chair/department head, it is in the social sciences, so you will want to check with a trusted person in your field for some verification on specifics. However, I think she has some superb advice in general about writing compelling and concise documents.

By "leave the course", did you mean quitting the PhD altogether? Have you considered switching labs/advisers at all, or even programs within your department? Is there any collaborating PI/anyone on your committee who may be willing to take you in (without affecting the fellowship)? I don't know how your program handles this, but I've heard of a few people (across different schools) who changed labs in their third year while staying in the same program. In fact, it might be a good idea to get a co-mentor even if your adviser isn't acting negative, since she's retiring and you don't want to be left stranded if you don't finish your PhD in the next 3 years.
If you are staying though, it seems your relationship/communication with the adviser needs some serious rethink. Perhaps you can try to figure out what specifically could have caused her behavior towards you to change for the worse, besides the dispute over that instrument. Has she shown such a negative attitude towards anyone else? Could you have upset her with something that you thought was unimportant? Or was it something that happened to her? Is she struggling with funding? Is there anyone in the lab who has been here longer/knows her better who may be able to help you out?
My other thought is, she must have taken you on as a student for a reason (she liked you during interviews, she generally likes mentoring, she wanted cheap labor, whatever it was). So if the relationship itself doesn't seem remediable, I'd still try to find out how you can be valuable to her/to the lab, so that she will have to respect and work with your regardless of her personal opinion (which, of course, will be hard as she's not providing you with the means, but maybe possible?)
On the other side, if you leave the program (presumably with a master's), do you have any plans?