biotechie

The same goes for me; I'm currently done with my first year (and all of my coursework!!!!) and am prepping for my qual proposal and defense. In short, I'm having a ton of fun (and no, that isn't sarcasm) and am loving my projects and being a graduate student. I have a couple of blog posts I made for students going to interviews; you can get to them through my profile. If there seems to be enough interest by mid-September, I may generate new blog posts about applications. You'd be surprised at the stuff you don't think to prepare for! Obviously I need a periodic break from studying and writing, so I figure a good way to take a break is to help/talk to you guys! I'll lurk here, or you can message me.

I have access to my Dad's netflix, but I also take advantage of my Amazon Prime Instant Video. Sometimes there are things there that aren't available for streaming on Netflix. I have cable, but I never watch it because my schedule is too weird. I was cheaper to get Internet + cable than it would be to have just Internet. Right now, I'm staring on Heroes since I have a week or so before I have to start my Qual proposal hard-core (yikes!). I also recommend House, Bones, and Once Upon a Time. I'm going to be coming back through this list to pick new things to watch.

I agree with this. I'm on an intramural soccer team (never had played before) and I go to Zumba. The weeks I don't work out, my body hates me. I get to socialize, escape the lab for a while, and stay sort of in shape. It is much better than having back spasms and feeling haunched over all the time.

I'm in STEM and I actually feel like I have more free time, but I'm also more organized with my time. I'm finally realizing (after undergrad and a MS) that how I manage my time and plan my experiments are key. I'm getting more experiments done, but I have time left in the evening that I use for relaxing and sometimes reading more papers. I'm already done with the coursework part. I've also been finishing things way earlier than I normally would; I used to procrastinate until the last minute for papers and applications. Now, my abstract for my qual is due in a week and a half. I have it done and mostly approved by my PI... just waiting on edits. It is kinda weird having time to myself on weekends. I still go into the lab to make sure my mice are happy and tend to cells, but I get time for me.

To add to this, I didn't contact any potential PIs until interviews. I got interviews at 4/6 schools, and the two rejects were major reaches for me, anyway (anecdote: don't put the wrong school name in your application to WashU. That = reject for me ). Once I got to the school I ultimately decided to attend, I found that there was a new PI doing some really cool things (outside of what I thought my interest area would be), so I ended up not even rotating with 2 of the POIs I'd picked out. So I think you should do as you wish, though it might be wise to be sure you're going to apply to that school before you contact the POI. I saw a mention of the subject GREs. Most schools "recommend" them, but few require them. Only take it if you're switching fields or you've got some grade discrepancies/lots of time off from school. I didn't take it, and I was told it didn't hurt my chances at schools. Most students in my new program didn't take the subject GRE. My point is, you may not need (or want) to fork over the cash for that extra exam, just the general exam. Just like what Glow said, feel free to message me questions. I applied to: UW Seattle Immunology (rejected me) WashU DBBS (rejected me; obviously Glow will be the WashU expert) Baylor College of Medicine CMB (Now called IMBS) UCSD Biomedical Sciences University of Florida IDP in Biomedical Sciences University of Utah Applications seem scarier than they really are; you'll be fine.

So far, it hasn't been an issue as I can do remote access to my school PC to do the things or use programs that my mac doesn't like or that I don't have on my mac. Most programs have a mac version, so if they're not too expensive and you don't have remote access capabilities, you can go that route. I like the remote access route because then I don't need to constantly keep a backup drive with me to shuttle between the computers. You should avoid cloud systems unless you can ensure they're keeping your data safe and encrypted. Some molecular biology students have access to patient data, so you likely won't be allowed to use the cloud.

I think you should give them a shot. You could also consider applying to interdisciplinary programs which will give you more flexibility to choose professors. In some cases, that means you could rotate with faculty from biophysics AND then do your next rotation with someone in biochemistry or molecular biology. Just something to keep in mind.

Keep in mind that some labs will issue you a computer, and if they do that, you won't need a super powerful laptop. I used a Mac in my old lab, but my new lab uses PC, and I was given a desktop to work on. Half of the time, I'm using remote access on my 13in retina macbook pro when I'm at home to do work on my Windows computer in the lab; I have programs installed there that I didn't want to buy a license to have on my own computer. Just make sure you have a good processor, 8+ GB of ram, and a decently large hard drive (I've got 1TB). I've switched over to using solid state drives as my last two drives crashed after only a year or so. SSD's don't last forever, but there isn't so much moving around mechanically, and I feel like things open faster. If you're going to be doing lots of modeling, there are additional graphics things you need to work out, but I don't have info on that. I really like the retina display on my macbook pro for editing/viewing fluorescent images I've taken of cells and tissues, and there are lots of PC laptops with screens as good, too. 8 GB of ram is good enough for me to run photoshop and a bunch of other programs simultaneously, though it does sap my battery. Normally it lasts 7-8hours, but with photoshop running, it is down to about 4. If you're taking it to and from school, make sure it is light enough and small enough to be easily portable. I ride the bus and I'm small, so I didn't want a behemoth laptop. This one is fine for me.

To add to what GeoDude, Takeruk, and rising_star said, I agree with the "don't worry so much" part. I came into the PhD program I am in now with a masters degree, and I haven't had any problems where I needed to "catch up." My masters coursework was enough to help me not struggle through my coursework, and this was in a PhD program which puts all of the classes into the first year. As far as joining my new lab, there was no catchup for me because I've done the majority of the protocols we do in a research setting (including troubleshooting). If you really have as much experience as you seem to be trying to say, I think you're not going to have anything to worry about. Publications seem to be something that all MS students are trying to strive for before PhD.... which is silly. As GeoDude said, it can take at least 3 months for reviews to happen, and that doesn't include revisions, which can take up to a year if you have additional experiments to do. The work I did as an undergrad is just being published now (1 year into my PhD program, 3 years after I did the work), and only a portion of my MS work has been submitted in a manuscript, which is currently being reviewed. These people understand that publications take time, and they're not going to expect you to have a CV with 5 publications as a 1st year graduate student. Also keep in mind that you're going to be coming into the program with a variety of people with different proficiencies. I interviewed with a girl who had her JD, but hadn't had molecular biology since undergrad, with a 6-month internship in a lab as her experience. She got in, and last I talked to her, she had successfully completed her first two semesters. Classes are designed to challenge you, yes, but they're also to make sure that everyone is up to a certain threshold of knowledge by the end. The students I was in classes with had less research experience than I did (6 years in my case) with the lowest being a summer internship. They also had not taken as many classes as I had. Sometimes they scored better than me, but I never worried about not passing. Having the research experience of a 3rd or 4th year graduate student means you've put in at least that much time in the lab and have generated manuscripts, grant/fellowship applications, etc. Be careful about saying that if it is not really true; you're a MS student, and though I don't think telling you to do this will get you to do it, you shouldn't be comparing yourself to other PhD students until you are one. Don't compare yourself to a student who has been in the lab for 4-5 years when you've only been there for 1... they've got more experience than you do. GeoDude is right when he talks about admissions. I had professors who knew how I was in the lab and who wrote me awesome letters of rec, and my research experience spoke for itself, even though I did not have any publications at the time of application. I talked about these experiences in my research statements, and my professors talked about my lab work in the letters. When I interviewed, they wanted to know all about my MS thesis project, and I willingly took them through it. When you join a lab at your new institution, you're going to throw a lot of that research out the window; I joined a lab that does metabolism, and I came from 6 years of transcriptional regulation and cancer biology. As far as loneliness goes, once you take a step back and stop trying to cram an entire graduate career into a single year, you need to take time to do something that isn't school or research-related. I play on an intramural soccer team for the university across the street, and some fellow grad students and I have a move night every Monday night to give us a relaxing start to the week. After my qual, I will teach a intro to lab class for little kids and play my trumpet in one of the local ensembles. If I find myself getting stressed, I call my boyfriend (13 hours away) or find someone to hang out and study (or shop on a weekend). Do yourself a favor when you go for PhD: even if it costs a little more, so long as you can afford it, live closer than 30 minutes from school. I'm a 15 minute drive, 30 minute bus ride, and if I were any farther, I'd be ripping my hair out. Some people deal well with being so far away, but for me, it would stress me out a ton. Hopefully hearing similar things from all of us will help. Please find a day to take a break and go do something fun, soon.

Orientation in my program was mandatory, but we also aren't allowed to have jobs on top of our studies.... I would do my best to attend orientation even if it isn't 100% mandatory. There will be things you think don't matter, but also tons of things you wouldn't think of. You don't want to inadvertently mess up your course schedule to screw up your qualifying exam or your teaching schedule, plus there may be more detailed descriptions of your requirements.

I second what juillet said. We also don't have vacation/sick time. Going home for a short break a couple of times a year should be fine. My PI literally told me I had to go home for a short vacation after finishing classes. Some PIs will verbalize that to you, and others let you come to them to tell them when you need to go for a break. As long as you're not taking long weekends all the time, you should be fine. As far as sick time goes, if something really bad is going on for you and you need time off to recover, talk to your PI about it. They may let you take a few weeks. If you're still in classes, you probably will have to take a leave of absence, but note that often times, you lose your stipend for that period.

I'm all for doing the thesis. It will demonstrate that you're not only good at research (your experience), but that you generate hypotheses and generated a thesis, so you're ready to step it up for your qualifying exam, grant writing, etc. I'm not in computational bio, but others in my interdisciplinary program are. I came into my program from a thesis-based masters, and I was told at interviews that that makes them view my application more positively than a non-thesis masters. This may vary by program, though! Even if the program doesn't want to see it, having completed that experience helped me a ton. I'm ahead of other students (even compared to those who did non-thesis-based) as far as being able to propose hypotheses, determine how to approach them, and write/defend that I wouldn't have gotten from being in the lab alone. My 6 years of research experience plus my thesis experience have me set up well enough that I'm well into preparing for my qualifying exam. At my practice qual with a proposal on a different subject, I felt more prepared to handle the questions as I had been through a thesis defense of my MS. Other students are not as used to presenting and defending. That being said, if you can get multiple publications BEFORE you apply to grad school, that'll look awesome on your application, and they might not care about the thesis. My thesis was in-prep when I was interviewing, but the school still said that the fact that I had to complete one for my MS stepped me up. Feel free to message me if you have more questions. I just survived my first year, and am now prepping for quals.

Survived my first year! Classes are over, and I don't think I have any more to take. So.... YAY! On to quals!

The reason they want to know where you decided to attend is likely to do with record keeping and how they asses the success of their own program. Most programs lump this data together and generate a report of which places the students that accepted their offer got accepted and rejected and which places those that rejected them went. It sort of unofficially ranks them and they use it to try and figure out why students accepted other offers over theirs. Sometimes this leads to improvements in only the interview process, but can also translate to changes in the entire program. They aren't likely to harass you about it. I gave the info to the places I turned down for interviews and the offer I rejected, and they haven't bothered me since. That being said, you are allowed to tell them no!

Don't freak out. Just roll with it. Find ways to make your planning fun! That's what I had to do. Keep in mind I was also writing a MS thesis and working in the lab in the midst of my preparations to move.... and lost contact with my PIs when they were out camping two weeks before my defense (note that they stay in contact normally, but one had been injured and airlifted out... talk about stressful). So my thesis defense was moved to a week before I moved to my new school. I had to keep things fun so I didn't stress out. The sudden stress of not knowing when or if I was going to get to defend before I moved also kind of snapped something in my brain. I was stressed initially, but I learned to go with the flow. If it was going to happen, I was ready for it. Turn everything into an adventure... and try to prepare for it. Lists are your friend. Plan fun things for a few hours on the weekends. Take the time to find guides about fun things to do in your new city, and schedule them into the days when you're moving so you have something fun to look forward to. The anticipation for me was the best thing, and once I got over the stress, I was able to embrace the excitement and the thrill of moving over 1000 miles from home. That said, now I'm at the end of my first year, almost completely done with my coursework, and quals are in 5 months. I'm not scared or stressed. I'm very Zen about the whole thing. There aren't very many unpredictable things anymore other than random mouse problems that will arise. Now looking back on moving, getting things set up, starting classes, and going through rotations, it really was a lot of fun, and the most stressful part was my parents getting mad when I couldn't decide where to put my desk. If you have specific questions about prepping to move, etc, hit me up. It's easier to be able to talk to someone on the "other side" than to all group together and compound your worries about the unknown!

I will be posting up a new blog in about two or two and a half weeks, once my coursework completes. What information would be useful for you guys from a student nearing the end of her first year? Coursework is wrapping up for me and I am starting on my qual. I know there are still questions on backup plans, but also for those of you that have a destination already, how you afford to move, when to move, and what to expect in rotations. I'd rather tailor it to what you want to know. Feel free to message me if you would rather not post your question, here. And congratulations! You've survived applications season without exploding!

I will also marginally disagree that you really need to go somewhere else (as a first year who is currently prepping for quals and is in the midst of grant applications). I stayed on campus. My letters of rec were from a professor I took a course from and helped with a small project, my co-PIs from my lab (which really should have counted as one PI + one collaborator), and an administrator at my undergrad (who vouched for my student mentorship). If you can research and gain strong skills within the lab you're in, why can't you work hard this summer and stay in the lab during the school year? I went into PhD applications with 4 years undergrad research experience, plus 2 years masters. I stayed on for a masters because I had a really cool mouse model I didn't want to leave. Yes, I worked in two different laboratories, but the first was out of field. The things that made me stand out on my applications were internal research awards that I won, mentoring younger undergraduates, and the fact that I learned so many different techniques to the point where I can apply them in any laboratory without needing to look up the information. You don't need to have a publication to get into graduate school. That's actually a requirement to GRADUATE graduate school! Yes, it would look nice, but you mostly just need to demonstrate that you're passionate about research though your application materials and letters of recommendation. You also have to realize that sometimes papers aren't published for years after your research experience. The research I did as an undergrad 4 years ago is just now getting sent to the presses. You learn some things with a year straight of research experience (or 5, in my case) in a single lab that you're not going to get skipping around from place to place all the time. Techniques like qPCR can be learned anywhere, but things like primary cell isolation and culture take some time and dedication that you can't get in only 3 months, and these are skill types that will make you stand out. There is also a sort of Zen to research. You may be trying to do something 20 times in what you think is exactly the same way, and then like magic, you learn and you don't know what is different. That comes with experience. See if your potential PI would let you stay on during the school year if at all possible. If you can work for the three months, then the school year AND collaborate with another lab group, that can be just as powerful as an external research experience, and you'll be able to get a letter of rec. They want applicants who can DO science... showing you can work in the lab well and collaborate are two huge things that are going to give you some points. Add some small internal or external research dollars that you obtain to a decent GPA and GRE, and you're golden. That isn't to say that external research experiences don't have their merits; you can spend time in a high profile lab, which can be a big deal. From experience, though, students who only do REUs in the summers with little or no other lab experience come into graduate school with a much narrower view and understanding of research than students who work in a laboratory for a year or more and actually get their feet dug into a project. Those students see more of what goes into the project, and they may actually go from troubleshooting to completion of a small project. REUs rarely complete a whole aim of a PI's research grant, but in a year, you could have a chance at it. Please don't do things only to pad your resume. Make sure you're getting relevant skills and experience out of it, and not just a letter of rec. With all of this, I think it comes down to two choices: 1. You can stay at your PI's lab over the summer, work your butt off, and try to stay in the lab in the fall and collaborate with another lab. Try to take a relevant course like a paper/journal course in an area you're interested in or a good stats course. 2. Do a summer research experience elsewhere (which can be expensive if it isn't funded!). Please feel free to message me if you would like, Flux.

I'm one of those crazy people who spends 10 hours at school a day because I'm excited about my experiments. I still get about 7 hours of sleep when I don't have projects due. Lately, since I'm still in classes, I've been getting less, but I've been promised it will be easier to get the sleep once classes are over. My typical schedule: 7:00 wakeup/shower/scream at the clock 7:45 pack lunch 8 or 8:10 bus to school (45 minutes ride)... kill 2 birds with one stone by reading papers for lab... or a novel because I need extra fun. 9:00-6:00 lab, classes, and seminars 6:00 3x a week in the gym at school, 1 hour exercise (Monday Zumba, Wednesday Soccer with some of the PIs, Friday cycling) 7:00 Get on the bus home 8:00: Food, homework, papers, and data analysis. 11:00 or 12:00: Sleep time. Sometimes I'll run or jog on the weekends, but often times, I end up in lab because mice and cells don't work on a normal human schedule. I didn't plan out this schedule... it just sort of happened. I wasn't exercising well until last term when I started in this lab. The PI kind of helps motivate us to play outside and he understands that we need to do things other than pipet and vomit data in order to be successful. It may help you to get a buddy for not only exercising, but also studying. I don't memorize well, and it takes a while for me to get the concepts, but if I have to explain it to someone, I learn more efficiently and have more time than I would if I just stared at the page or rewrote my notes. I can't help you on the dating front as my boyfriend and I are long distance. If I want to look cute, I have time, but half the time I decide I'd rather read a fun book than fix my hair really nicely. Plus the lab likes to destroy my clothes. I see tons of grad students who look like they came out of magazines. I like to joke that they don't work hard enough, but they score extremely well in classes.

I'm in Houston right now... Depending on where you live, it is super easy to bike to the med center on Braes Bayou trail and you don't have to encounter really any traffic as you're not on the road. I'm a really small town girl. Houston is very big, but feels more small town depending on where you live. It is definitely way better than some of the other big cities I've been to (London, Paris, New York, Chicago). The bus system is very good. I have a car, but I ride the bus in. I'm also across the street from an HEB and down the street from a gym. If I really wanted to, I could get by without a car. You guys should take the time to talk to current students more about what it is like to live in the area before you make your decisions. Don't let the big city scare you away! It isn't my favorite place in the world, but I could have ended up in a city I would have hated much more!

I actually use a desktop application for Mendeley. I think it was originally browser based when it started up, but now is a desktop application. I only use the internet part to sync my notes between my computers. However, I just figured out today that I can do it on my external hard drive the same way, so I no longer even need the internet or my browser and I don't have to worry about running over my online "space." You're not screwed out of reading, citing, and annotating your papers when you're offline since you can have it store your papers in a specific place for you on your hard drive. The browser compatibility thing I was talking about was for the add-on that will pull the citation in for you. You don't even really need that if you have the DOI or PMID. Even if you only have the title + an author or two, you can get it to find the info. Endnote does have Mendeley beat, there, but I haven't had any issues. I like Papers, too, but I don't use it for my academic reading. I actually use it for my creative writing stuff. Yes, ERR_Alpha, it is free: www.mendeley.com And while I'm posting links, here's Zotero, which is also free: https://www.zotero.org You guys can look at the sites for yourselves to see what will and will not work for you since it is going to vary a ton. I would just try to get something free to start that will play nice with EndNote as it seems to be what the majority of people are using.

It really is pretty easy to switch. I would probably start with one of the free ones like Mendeley or Zotero since you can always export at least your citations from those into a format usable by Endnote. I use Mendeley and I love it for annotating things; it is the citation manager I used for my masters thesis. My new PI uses Endnote, so I can export the citations I have from Mendeley to Endnote when I need to write a paper with him. I... don't get along with Zotero, but I have no idea why, so I can't pass judgement. Mendeley gets along with Safari and Firefox from my experience. I currently use the online storage to sync my papers between my school and home computers, but I don't know what I will do when I hit the maximum amount I'm allowed to store!

For that, you're going to need to look into what the course requirements are going to be for those programs. Some undergrad bioengineering programs put very little emphasis on molecular biology and you may have only taken one or two classes in it. If that's the case, you might want to avoid a biomedical sciences program as nearly all of the coursework may be molecular biology based. On the other hand, if your undergrad was more like a molecular biology degree and the PhD program you're considering has nearly all engineering-only coursework, you also might change your mind. I think what you are going to want to do is go through and review what you've already learned and then look at the requirements for coursework within these programs.

I really need to stop trying to type things when I'm so tired, though in the whole grand scheme of things, CRISPR is still pretty new. The new paper on the structure and use of the use of different Cas9 mutants was what I was trying to get at. I'm fairly certain we were hit so hard with the CRISPR stuff in classes this year was simply because that's when it exploded. We weren't really questioned about what the original function of it was, but more application and how methodology differs between Cas9 and slightly older systems. It is also a really fun system to work with, and in ways is simpler (such as you always use the same Cas9, just new guides rather than having to make a new TALEN), but alternately, you can have a loss of specificity with off-target effects that you can mostly get rid of with other methods like TALENs. I've used both TALEN and Cas9 (currently working with D10 mutant), and I like both for different applications. To add to what Mono said: Reviews are great to get a general understanding of a subject, but make sure that you actually dig deep and pull out the relevant sources when you're writing up things for grants publications in the future. The last thing you want is for your grant to not be funded or your paper not accepted because one of the reviewers happens to be the guy who discovered something you're basing your research off of and you neglected to cite them! Since you're going to be doing a lot of reading to help you solidify what you know and need to know, it might be good to also start working with a citation manager to figure out which one you like, learn how you want to organize, and start annotating things that you think will be important. Nothing sucks more than knowing a certain paper is important and then when you go to write your document, you can't remember why you thought it was important! I love Mendeley, but other people like Zotero. Both of these are free and you can take citations and export them in an Endnote format if that's what your future PI wants you to use. What I like to do is read a couple of reviews to learn about something, and then I dump those into a review folder in Mendeley. Anything I needed from the review, I try to find the original source, and that goes into a folder that I actually pull citations out of for publication. I don't find myself citing the reviews often, but occasionally, when they suggest new interaction schemes, I will cite them.

Read up on the CRISPR/Cas9 system. Even though it is so new, I've literally been tested on it in every class as a first year this year. I'm sure next year will be no different! It would be especially helpful for you to learn about the structural stuff and the different uses for the different versions of Cas9. There's the normal version (with nickase and nuclease, really good for knockout and some recombination), nickase only version (nicks a single strand, useful for things like recombination), and a mutant that is nickase and nuclease deficient (think promoter "tiling" with lots of guide RNAs to block gene expression). There's also some really crazy stuff going on with iPS cells, which are also going to be something you're going to be encountering in classes, too, most likely. There are some cool new papers out on iPS cells and differentiation into heart cells and how some of these cells need to be altered mechanically. My favorite things to read about are novel gene regulation and knockout systems and nearly anything epigenetics. I also like looking at seemingly normal epigenetic abnormalities and seeing how those contribute to autoimmunity. You'd be surprised how much you can find simply by reading and data-mining. There's so much whole-genome bisulfite sequencing done, now, as well as lots of histone ChIP. There are also lots of mechanistic studies involving chromatin structure and specific conformations of proteins that a biophysicist might like. If none of those sound cool, you could always stalk your potential PIs' publications and get ahead of the game! Feel free to message me if you have questions or want more specific titles. I don't know much on the heart stuff as I learned about it in a seminar, but the rest.... I could discuss in detail.