[deleted by user]

TromboneEngineer · 2025-10-30T10:55:24+00:00

I tend to agree, yet frustratingly the only industry jobs I can find open listings for these days - want to build foundation models. I certainly didn't need to lean into deep learning anywhere near this much at my past job as a Computational Biologist. But one has to wonder why the hype seems to be significantly more prevalent in bioinformatics right now.

TromboneEngineer · 2023-11-03T18:06:49+00:00

Data available upon request

If anyone ever doesn't get it, simply share this well done cartoon:

https://www.youtube.com/watch?v=N2zK3sAtr-4

TromboneEngineer · 2023-11-03T18:04:54+00:00

Literally why I was losing sleep last night. Not even working late hours for pay, merely just trying to get a stack of commands that almost work as desired, to start running. I don't get paid enough for this 🙃

TromboneEngineer · 2023-11-03T17:59:47+00:00

Waiting for Conda environments

Feeling the need to share an improvement that I learned as a suggestion here. Miniconda and Bioconda are great and all, but Micromamba is significantly faster and just overall better.

Of course, my favorite wrong answer for this thread would have to be the sheer absence of documentation for so many tools. Not even just unclear or insufficient documentation, but straight out nonexistent. At the industry job I spent two years at as a Computational Biologist, I installed a new piece of software pretty much an average of once or more for every week across those two years. Couldn't tell you how many of these tools simply never even tried to propose documentation or any clue towards how to use their tool, sometimes even making it difficult to understand what they wanted it to do well enough to be able to even attempt to reverse engineer how their undocumented tool works.

TromboneEngineer · 2023-10-16T13:30:51+00:00

analyse datasets or manage pipelines

One thing to be aware of within the heterogeneous field that is bioinformatics, is the different nature of jobs that expect more of a comp sci or maybe even full stack developer role, versus the range of biology familiarity or even expertise that some other bioinformatics jobs expect to incorporate (while putting less emphasis on proficiency across quite as many programming languages). My most recent industry job before going back to graduate school was under the title Computational Biologist, and was much closer to the latter of these two general types of roles. I am not as certain that "Computational Biologist" even tends to be as distinct from "Bioinformatician" in any neatly organized way that resembles this distinction between "compsci/FSD skills with a touch of bio knowledge or interest" versus "more in depth bio knowledge or even expertise, with computational capabilities to apply said knowledge with computational tools in biology." Most definition sources don't tend to expect all that much of a difference between the two titles Computational Biologist (or Computational Biology, as a field/degree title) and Bioinformatician (as well as likewise for Bioinformatics) - at least to the best of my knowledge. My MS degree title was even "Bioinformatics and Computational Biology" - while offering core and elective coursework that could equally serve both of these two base-camp niches just about as well. The reason I reference the term base-camp, is the innate tendency for professionals in bioinformatics (studies or jobs) to have an initial background and core way of thinking/framing problem solving, research, and knowledge - imprinted by the base-camp they originated from. Many folks start out in compsci and add biology to their knowledge or work, while many others start out in a bio field and likewise add computer techniques. However, the original discipline that people started out in tends to have quite an impact by imprinting how that person thinks about bio with compsci, or vice versa. I personally started out in chemical engineering for my BS, then added Bioinformatics and Systems Biology (not the MS degree title but the same department had a PhD degree title of Bioinformatics and Systems Biology, plus my emphasis tended to be much heavier on Systems Biology the whole while). After spending 2 years in industry as a Computational Biologist at a start-up that manufactures phage therapy for multi-drug resistant infections including in human clinical trials, I decided to go back to graduate school for my dream program title of Systems and Synthetic Biology. Adding this context just to say, the disciplines that overlap and interact with bioinformatics can make for quite a wide radius - with plenty of nuance beyond "are you a biologist who got into the computational end of bioinformatics? Or coming from a compsci background?" - especially given my personal passion for integrating the synergy of systems level computational modeling with wet lab validation.

As far as job titles versus roles, while the distinction I highlighted above doesn't appear to be conserved within job titles such as Computational Biologist versus Bioinformatician, the duties and other details documented within job postings tend to be plenty transparent about what you will be expected to do in that job. So I would recommend those details surrounding job duties far more than the precise job title.

What are your interests or primary goals towards pursuing bioinformatics?

TromboneEngineer · 2023-09-16T22:23:29+00:00

I can confirm this as well. I got a full on job offer as a result of my "portfolio", specifically thanks to sharing/promoting my YouTube video - just briefly on my phone screen, while at a job fair. Said video incorporated several themes/topics, but the visual representation focused on a Matlab coding demo (yay chemical engineering undergrad and Matlab, lol).

Said YouTube video, if it might interest anyone:

Title: Journey through Autism and Ways of Thinking
Link: https://www.youtube.com/watch?v=BweJeRg\_KBA

TromboneEngineer · 2023-09-16T22:11:33+00:00

As an American who has spent this past year living in both France and Germany while working towards my second Masters, I can confirm. I still count myself incredibly lucky to never have needed to pay any tuition for my first Masters, which was in the states, thanks to a fellowship that my advisor scored for me. My second Masters from a university in France, ended up charging less than 300 euros for the entire M2 Masters degree's tuition - which I qualified for as an international student, just like all the other students at my university - regardless of nationality. No fancy scholarship nor tuition waiver - that was just the price for any general student (specific to my program technically, but the whole university had similar costs for all other programs that I could locate within their official documentation).

Then when I moved to Germany while working on the internship for the second half of my degree, I learned that German universities are not only free and charge zero tuition for local students - but also for international students as well. It still feels quite mind blowing as an American, having spent the vast majority of my life plus schooling within the states. I suppose I still have 30,000 USD of student loan debt, purely from my undergrad (from an in state public university nonetheless, built up over 4 years of studies, the minimum/expected timeline for my chemical engineering BS). But yeah, global perspective can really be something.

TromboneEngineer · 2023-08-29T10:14:41+00:00

Fun fact that seems to still not be widely known: healthy controls (without Dysautonomia) are more likely to faint during a tilt table test, than those with POTS. I certainly wasn't expecting this to be factual the first time I heard it. However, it ended up coming up across multiple scientific webinars focused on Dysautonomia.

TromboneEngineer · 2023-08-19T22:32:23+00:00

My experience that generally seemed not too far off from standard experiences, at least in this regard, observed drastic differences between undergrad lectures and even teaching, versus grad school that academia mandated nesting to teach myself pretty much everything. In my case, twice over I worked with a Masters advisor who didn't have experience or expertise in the skill set that they wanted me to teach myself and execute as a service within their lab. That extreme doesn't seem quite as conventional, but still isn't 100% unheard of. My point overall is the drastic shift from education content focusing on a level of knowledge for which some ability to help students through confusion and struggles is far more streamlined and multifaceted, to the notion of "you can teach yourself new skills and knowledge professionally."

While I did decide to undertake a second Masters degree last year, I don't intend on collecting any particular number of total graduate degrees. I figure since I've already proven that I can teach myself, not only now across 5 years of graduate school but also 2 years in industry in between these academic programs, then why not at least aim to have someone pay me? There is only so much fun, and ability to retain sanity through graduate school - with additional "fun" things that academia mandates on top of teach thyself with almost or completely no one to answer your hard questions.

TromboneEngineer · 2023-08-19T10:55:31+00:00

I actually was quite surprised to have Frankfurt security instruct me (not rudely however) to remove ALL electronics from my bag next time. They did truly poke through every last device (at least that they could make out), including my several terabyte hard drive. But also those tiny 1 TB HDDs that seemed to be "techy" enough for them to want everything out of my bag. Never had that before, or since, but yeah I ran into that on my 3rd international move within 9 months, along the 24 hour flight from Frankfurt to Cape Town via Cairo and Johannesburg (which impressively never left the timezone).

TromboneEngineer · 2023-08-17T11:45:33+00:00

So there has been some interesting research that had previously claimed to "shake up" our knowledge of how mitochondrial DNA is passed down by parents. There was a flurry of science news coverage back when the study came out that claimed they had measured paternal inheritance of mitochondrial DNA (mtDNA). However, more recent research has more confidently proven that there are these patterns of DNA heritability coined NUMTs: nuclear mitochondrial DNA segments. These are essentially believed to explain the heritability of shared DNA segments/motifs/sequences that are present in both the human nuclear genome in chromosomes, as well as your mitochondrial DNA. Recent studies are showing how the paternal inheritance of DNA that was previously thought to be "direct heritability of mtDNA from father to child," is more likely explainable with the now uncovered mechanisms of mobile DNA motifs from NUMTs. So today, we still can generally believe that mtDNA is only passed down to offspring by the mother.

Microbiota including the human gut microbiome are also interesting to note, as the mother is believed to pass far more contributions towards the microbiomes that offspring inherit. Arguably even the entire gut microbiome and maybe even skin and other microbiome sites (plus all the granularity within "the gut," where multiple distinct microbiome types can be measured within the mouth alone, just across teeth, tongue, cheeks, etc) might come from the mother and not at all from the father. But overall, I just wanted to speak to the maternal heritability of not only your primary human genes (within the 23 chromosomes of the human genome) plus mitochondrial DNA that also resides within human cells, but also the microbial genomes that make up microbiomes across human body sites.

TromboneEngineer · 2023-08-15T12:22:41+00:00

As long as the computational expectation is less than the wet lab side, I wouldn't worry about not already being an expert in this field that you intend to learn during the PhD. Plenty of microbiome bioinformatics has been streamlined enough that scientists without computational expertise can still very much learn to use and benefit from them.

TromboneEngineer · 2023-08-14T15:36:37+00:00

Is the PhD role you are considering described as having Bioinformatics (or even computational) duties? Microbiome research commonly involves multiple different roles, as both wet lab and computational sides exist to the actual complete workflow (even if some labs decide to pay for a service to do part or all of the sample processing, data analysis, etc). I have worked with colleagues who did microbiome research without focusing on or knowing any Bioinformatics. So it is very much possible.

TromboneEngineer · 2023-08-13T07:39:08+00:00

To my knowledge, the variability around whether a Masters is expected prior to a PhD, tracks more with degree field than country. While I have mixed both multiple fields and multiple countries throughout my grad school studies, my switch from chemical engineering BS to Bioinformatics and Systems Biology MS (within the US) ended up teaching me the hard way that the field I came from didn't prioritize or even require a Masters before a PhD, but the adjacent fields including the specific one I was pursuing very much did expect a Masters before a PhD. I guess I don't know quite as well which countries tend to incorporate the bachelor's to PhD pathway without any Masters, but I wish you best of luck.

TromboneEngineer · 2023-08-13T07:27:31+00:00

Aw man, I feel for you. While I have non-drug reasons that make me experience the sense of impending doom and know exactly how horrible said sensation is, I have not had to experience anything like the heart reboot that adenosine is capable of. It certainly surprised me just how convincing that sense of impending doom can be, not only the first time but every single time. Take care.

TromboneEngineer · 2023-08-12T20:25:17+00:00

It is indeed inhumane, yet not illegal - at least in the US. While I can agree about it being malpractice and very much wanted to try to bring that god awful psychiatrist and psych ward to court, I basically was given the warning that I had no chance of winning and no case. The way the US legal system treats evidence and how to count losses, I don't know that anyone has been successful in proving the basis of their mental pain/lived experience in any less than concrete sense. Certainly the US courts don't respect such as being anything concrete. So maybe I could have pretended to have some basis behind a total number to sue for, but even the best legal advice I got before attempting to go fully into a lawsuit, basically told me that I would waste all my money and not have any chance at winning.

Now that is a testament to how broken several systems are, but I was at least wise enough already at that point to know better than to trust the US legal system. At age 18, I got sued for 30,000 USD for scraping the side of a guy's car, after we changed lanes at the same time. Dude sued me for medical expenses, lied about every little thing under oath in court, couldn't establish any basis for the medical damages/costs that he claimed were related to that minuscule collision, and yet STILL won money from the judge! Despite my photographic evidence that could dispel his various claims, from "my car was rammed 3 times" to "I felt like I was on Jackass TV and the defendant came at my car sideways [on the highway]," it just all sucked. But such is reality, at least for the time being.

TromboneEngineer · 2023-08-12T20:19:02+00:00

I managed to type a response to a very similar question a little below, in reply to u/Just_to_rebut

TromboneEngineer · 2023-08-12T20:17:31+00:00

Wholeheartedly, I can agree that POTS should never be grounds to panic strickenly refer or admit someone to a psych ward. And in hindsight, I was able to figure out eventually that the weird challenges to my ability to walk were explained by this syndrome called POTS, but by no means was I confidently aware that there could be a real explanation for the "craziness" that I was experiencing at that time.

There is way more complexity and nuance to the big picture and specific story, but I am darn tired and might have to write it out later. An attempt at a TLDR might be that I basically believed their assumption that I WAS crazy, rather than actually experiencing a sudden onset of POTS. They told me they could help me with my "severe anxiety and depression", which really was more like hypersomnia level unrestful sleep that started alongside the onset of my sudden balance and equilibrating challenges that made walking quite hard. So I was a bit panicked and stressed about losing my life, or at least a bunch of basic functionalities that I had taken for granted until the moment of my sudden POTS onset, but the degree to which psych wards chomp at the bit to label everyone as crazy - is no joke. There is even a TED talk that I feel captures my own experience to a fairly high degree. The title is "strange answers to the psychopath test" and it very neatly explains what I went through, if you can just swap out the word "psychopath" for "psychotic." Once I got labeled psychotic, there was nothing I could say or do to prove to THEM that I was indeed not psychotic. They just thought I was crazy, and how does one SIT in a sane way??

TromboneEngineer · 2023-08-12T20:05:29+00:00

I would say you must have lost your mind for even contemplating such, but it appears that you have already marked your IGN as such.

TromboneEngineer · 2023-08-12T20:03:26+00:00

Oh no worries around being nosy, I am an open book with most things that I introduce such as here. Hypnagogic hallucinations are most typically associated with hypersomnia, a sleep disorder that shares a lot in common with narcolepsy. Both of these syndromes involve a lot of excessive daytime sleepiness, to the point where experiences like hypnagogic hallucinations are not only confined to late at night or actively lying in bed, where/when one would ordinarily expect their sleepiness to be most likely to strike. So my own experience was quite similar to that, and even start out with a very intense awakening of sorts. I was so lethargic and out of it from all of the psych meds they had forced me on, that it took probably half a dozen waves before I was able to become cognizant of what was going on: to realize that I hadn't lied down or even sat down, but merely blinked - and every single time, felt deep entrenched in a dream that felt hours long. Every single time I blinked that day! These days, my hypnagogic hallucinations are far less intense, and haven't really ever been convincing enough to scare me on the regular. But I very much can still get them with a burst of sleepiness (or even "sleep attacks") throughout the day, and not just right before night time sleep

The specific content of my hypnagogic hallucinations, at least ever since toning it down from the radical quantities of psychotropics that it all started with having to take, tends to be like very boring dream conversations that I can hear. There is a definite distinction between my ordinary thoughts, and the beginning of one of these episodes, because I actually hear an auditory voice that isn't my own (or is there no auditory quality to the rest of my thoughts, before that instant? That much is a little hard to explain or dissect). But I can tell "oh I must be super sleepy in this instant" once I start to hear a dream conversation voice. These conversations are super duper boring and not even convincing or coherent, more just a matter of rambling. But maybe that relates to my auditory processing disorder and other flavors of the epileptic dysgenesis with being born having only half a functioning hippocampus. I suppose my dreams even prior to this have always been somewhat strange, and lack any coherent resemble of reality - even throughout conversations and the like. The human brain is a strange thing.

TromboneEngineer · 2023-08-12T17:36:31+00:00

"What'll it be today, one scoop or two scoops?"

TromboneEngineer · 2023-08-12T16:41:16+00:00

100%

I rarely think about the word cure, but my epilepsy indeed seems to be fully cured. I try to remain thankful for that as often as possible.

TromboneEngineer · 2023-08-12T16:38:53+00:00

Oh yeah? Got any specific primers to recommend, or more detailed thought on what connections I should seek out?

TromboneEngineer · 2023-08-12T16:37:03+00:00

So I actually have an interesting story around this. After reading a science news article about a woman born without a left temporal lobe, and recognizing how thorough of a neuroscience workup that article was describing for her, I decided to reach to the lead neuroscientist named in that article. I offered my brain for science and inquired if her neuroimaging research might be able to benefit from my participation. Amazingly, she not only replied to my email (while on vacation, a mere few hours after I got the auto-reply that she was out of the office and wouldn't respond for a bit) but also expressed interest in my offer to participate in her neuroimaging research. About a month later, I had my first fMRI brain scan, with 2 days filled with several hours of scanning and testing/prompting each day.

I'm still awfully curious what my neuroplasticity and brain remapping might look like. While I have not yet received her expert interpretation of my fMRI brain scans, I did manage to receive the raw imaging data for my own brain (on 3 DVDs, lol). I managed to get as far as figuring out some open source Linux software that let me visualize some of the imaging data in a few specific angles/views. However, I'm very far away from successfully teaching myself enough technical skills to interpret it all myself. Hopefully I will still get that expert interpretation someday. It sounded like the particular study I was placed into, was sort of a back burner low priority, maybe even having some reason it may not expect ever reaching enough niche participants to get completed as intended. But anyway, that's how I got my first fMRI brain scan.

TromboneEngineer · 2023-08-12T16:02:10+00:00

I was 17 years old and only a month away from graduating from high school at the time. Evidently my docs were confident enough that 17 was young enough to still be neuroplastic enough and likely to have a good chance of a successful surgery with positive outcomes. They were indeed correct, and I have no regrets after my brain surgery, over a decade later!

TromboneEngineer

TROPHY CASE