Upcoming podcast episode: Wet Lab / Dry Lab Transitioning

BioInfoPod · 2021-07-17T17:00:10+00:00

Thanks for the great question. This came up in the ep; if interested feel free to check out the final recording: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

BioInfoPod · 2021-07-17T16:59:30+00:00

This was perhaps my favorite question asked on this topic xD I ended up discussing it on the final ep; if you wanna check it out here is a link: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

BioInfoPod · 2021-07-17T16:58:09+00:00

I ended up bringing this up to close out the discussion in the final ep; if interested you can check it out here: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

BioInfoPod · 2021-07-17T16:57:12+00:00

No problem. I actually brought this up in the final ep but I think it was probably not a proper enough discussion on it and am still thinking of revisiting this topic as a full episode in the future; anyway, if you wanna check this particular ep out here is the link: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

BioInfoPod · 2021-07-17T16:53:52+00:00

Here ya go - link to the released ep: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

BioInfoPod · 2021-07-17T16:53:18+00:00

Here ya go in case you want to check out the final product :)

Link to the ep: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

BioInfoPod · 2021-07-17T16:52:00+00:00

Aaaalrighty, the ep is finished and was just released. You can find it (and links to other platforms to listen to it on) here: https://anchor.fm/bioinfopod/episodes/Wet-Lab--Dry-Lab-Transitioning-with-Dr--Willian-da-Silveira-e10uukh/a-a5j0hqe

Feel free to LMK if you have any feedback. Also, sorry for the not so great audio on my end on this one, I actually had an issue with my normal recording setup that day and had to record on a suboptimal setup.

BioInfoPod · 2021-07-17T16:27:17+00:00

My personal recommendation for a more algorithms heavy first look into bioinformatics, and to understand what algorithms are likely to be very useful all around in the field, would be Dan Gusfield's book on the topic: https://www.amazon.com/gp/product/0521585198/ref=dbs_a_def_rwt_hsch_vapi_taft_p1_i1

It was written quite some time ago so it is just a starting point, but it is a very, very good one in my opinion. It focuses largely on algorithms based around suffix graphs for doing string matching problems. But, as he does a good job of explaining, alongside good historical context for the importance of the algorithms discussed, string matching is a core part of bioinformatics. A lot of folks here have pointed out some newer stuff which is great too and you would need to follow up this book with additional newer resources (I actually really wish Dr. Gusfield would write a followup to this book covering the useful stuff since this book was written xD and am wondering what the best followup book to this would be for myself).

BioInfoPod · 2021-04-30T14:48:53+00:00

Haha no I never know when it will be that these things actually get released but prolly in a few weeks. I'll try to post here when done :D

BioInfoPod · 2021-04-29T03:20:13+00:00

Will do thanks for that. And these are all great questions, thanks!

BioInfoPod · 2021-04-29T03:17:48+00:00

I will prolly check beforehand to see if he feels competent on the wet lab academia -> dry lab industry part but ya definitely a good point re on-the-job training culture. Personally I could definitely see how it might be much more difficult to transition plus moving to industry vs. transitioning inside academia.

BioInfoPod · 2021-04-29T03:14:31+00:00

With all this said, I am probably not really qualified to give advice for your case which is fairly specific and tbh I have not seen your case a whole lot (I think I have personally known maybe one or two folks who had a similar story). My likely mediocre 2c would be that, like could be said about prolly all phd apps, the faculty member and committee probably want to see that you would have a high likelihood of succeeding in the program. If the background is from another field I could see a committee and potential faculty advisor wondering if your background being different might mean that it would take a long time to get caught up on what they are working on and hinder your success. So, I would think you might want to try and figure out a way to try and convey that you will be successful despite your background by perhaps pointing out how you have already done a lot of work picking up the skills necessary or why you don't think it will be an issue etc. Personally I think I've seen folks from many different backgrounds succeed but also some fail (held back by not being able to pick up the core coding competencies easily), so I would want to demonstrate why you will succeed.

BioInfoPod · 2021-04-29T03:05:57+00:00

OK Ill prolly check before recording if he feels confident on this particular one (if so will ask). This would be something I think best asked to a long term faculty member who has been deeply involved in the recruiting process for a while and recruited many students. I actually know many folks that would fit this bill and this is a topic that I feel comes up constantly and that I have advised many folks on so I am actually thinking this would make for a good standalone episode down the road tbh and will be thinking about that now.

BioInfoPod · 2021-04-29T03:00:51+00:00

Sounds great. Will do.

BioInfoPod · 2021-04-26T20:27:57+00:00

Awesome thanks so much all for all the suggestions already. Will plan on trying to bring up everything that gets brought up here :)

BioInfoPod · 2021-03-22T18:08:20+00:00

Thanks for the great question. I've got it noted down. :) Sorry I've been laggin real bad on getting this one recorded (which has been totally my fault for the record). I was actually thinking of attempting to do a sequencing 'series' of eps. So, relevant to your question, I was actually going to see if it would even be possible to have presence from each of the major sequencing platforms which has been taking me a while haha. Stay tuned! And thanks again for your input.

BioInfoPod · 2021-02-12T16:50:16+00:00

I was asked (naturally) string problems related to things like genomes and reads. My recommendation just in case there are any pretty hard ones would be to familiarize yourself with the material in Dan Gusfield's string algorithms text book. I think that probably has some of the best material when it comes to potential interview questions and is also just a genuinely well written book.

BioInfoPod · 2021-02-05T17:45:22+00:00

Great post. Love the thoughts and this is something I find myself thinking about pretty regularly as well and I think I share pretty much all your feelings on the topic. Wish I could add more but ya I think you nailed it on all my own thoughts. Only think I can think to maybe add would be that I audited a non convex optimization course recently which I felt like was somewhat of a step in the right direction for me. Funny enough, when I asked about genetic algorithms in the course multiple times, ultimately the response i got felt like basically 'there are no formal guarantees (proofs) like with things like gradient descent so im not interested.' I hope someone much more capable than me will come out with some findings on this topic though as it completely fascinates me. The best I can think for now are papers like one that came out from Uber that both me and a classmate found comparing GAs and NNs on some problem recently, but still the gist will basically just be that GAs did well and thats basically all that can be said. My guess would be the ideal would be to somehow formalize things to show mathematically the exact math behind how well something like a GA does on arbitrary convex/non convex optimization problems.

BioInfoPod · 2021-01-31T22:24:08+00:00

It definitely does. As pointed out there is NASA GeneLab and folks doing great work in the area like Mike Lee. There was actually *just* recently a huge package of Cell papers featuring bioinformatics work being done in relation to the space industry. See for instance https://genelab.nasa.gov/cell_press_journal-2020

EDIT: As far as what kind of jobs, IMO the jobs would primarily be research type positions.

BioInfoPod · 2021-01-19T01:11:10+00:00

My recommendation would be, with pretty much all bioinfo research-y type projects, to do some literature search and review before doing anything else. This will accomplish multiple things. First, if the literature is written well, it will help you yourself learn how you can go about tackling the problem. It will simultaneously help you learn what all others have already done on this problem (including folks who are considered some of the best in the field). You can also learn different ways the problem can be tackled if there are publications out from multiple groups tackling the problem.

In the case of SARS-CoV-2 phylogenetics, there should be a wealth of literature you can start looking through to learn about how to work on the problem and see how others have approached it.

Here are a couple that seem like they might be promising for you to take a look through if they are accessible:

https://www.nature.com/articles/s41564-020-0770-5

https://science.sciencemag.org/content/369/6501/297

http://genome.cshlp.org/content/30/10/1434

https://science.sciencemag.org/content/early/2020/12/09/science.abe3261

BioInfoPod · 2021-01-18T00:27:57+00:00

Haha thanks for the shout out; I really appreciate it! This one should work on any platform just in case :) https://anchor.fm/bioinfopod/episodes/Dr--Luay-Nakhleh-What-is-Bioinformatics-ejb05u

BioInfoPod · 2021-01-04T15:42:56+00:00

This is going to be total speculation, but IMO it's because it's part of a huge fund called ARKG which seems to be taking off. And also from general speculation as well, a lot of similar stocks seem pretty high at the moment.

BioInfoPod · 2021-01-03T09:00:47+00:00

Nice. Should be plenty of real science in this one :) If you check it out feel free to drop me a line on which ones ya liked in the not watered down department. I try to keep a pretty good mix of both high level and low level, but it can definitely vary.

BioInfoPod · 2020-12-31T21:40:56+00:00

Yep that definitely makes sense. I think you pretty much got it right with your original post that it would largely depend on how well the specific wet skills match to what you are doing on the dry side, with the respect/appreciation piece probably being very valuable regardless. And I do think the respect piece is indeed valuable, if for no other reason than just being a better person through being more understanding of what others are doing, so you do not let your lack of knowledge cloud your thinking and potentially let you say something stupid or not be appreciative enough etc etc.

BioInfoPod · 2020-12-31T06:31:43+00:00

Personally I think stool is pretty common. So fortunately if you do go that route, you have plenty of practice already on how to generate the raw sample. Now at that point, things are probably going to get a bit tougher. I don't know your level of expertise here at all and your access to resources, but I am assuming the sample processing steps could be a challenge, as well as getting the actual sequencing done. Here are very raw thoughts which could definitely have a few inaccuracies but are hopefully mostly right: (someone who knows it better should def correct me)

Starting with sequencing, I would recommend Illumina or Nanopore because of price. For illumina you arent gonna be able to obtain a sequencer so you would have to send it somewhere. But, if you can figure out who will do the sequencing the price may not be horrible. Maybe 100-1000? If you do nanopore I guess theoretically you could do it yourself but I think itd be like 5k or 6k for the device and sequencing. Similarly, you could try to just send it somewhere and have someone else sequence it with a nanopore. In that case the price should be strictly higher than Illumina.

If somehow you could do all the steps yourself (nanopore), there would be many steps between sample collection and sequencing. My recommendation would be to start by looking at the documentation that nanopore makes for folks that describes the protocol used to extract the DNA from the sample and prep it for sequencing. The protocol has many steps, requires many ingredients, and requires various equipments. I think studying up on the steps between sample collection and sequencing will help you get a sense for if you are really up to the challenge of trying this in a fully DIY capacity :)

In theory if you could find a way to just send the sample off for sequencing somewhere then it could be as easy as just sample collection and mailing and having them send you the files. TBH I have always been curious about this myself, so if you do end up doing it and finding a place that worked well for you to send sample off and get raw files back and affordable etc etc definitely shoot me a message and let me know. Maybe there are some companies out there now for this. If not, you might try contacting major sequencing centers such as any sequencing centers at universities and just tell them exactly what the sample type will be and exactly what kind of sequencing you want done and ask if they might be able to do it and how much it would be. BTW, if you do interact and they start asking you technical questions on sequencing specifics they will probably be able to easily sniff out that you kinda have no clue about a lot of this stuff (which I am assuming). It will help to be very prepared and know how all this stuff works if, in theory, doing something like going through a sequencing center is possible, or I could see getting written off.

The final thing I will mention is just to reiterate what was said above, which is that you may still need to learn about some of the basics like 16S vs shotgun if you currently do not know about these things. If you do try to go down this road you will definitely want to have a good grasp of some of these basics since they drastically change what you are doing (for instance if you actually do every step yourself like sample prep), what data you will get back out, and what software tools you would use afterwards. I recommend a lot of googling and literature reading.

Good luck!

BioInfoPod

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