LifeIsBio

A little tangential, but learning to code through video games has always seemed like one of the best ways to do it, particularly with friends.

> It is not the neat and cut world of science research.

You had me up until this last sentence. Everything I've experienced in science research is the opposite of neat or clean cut. Actually, I think I do my best programming and debugging with a treat it like a science experiment.

That's super interesting. If someone asked me if bioinformatics was complex, I'd say "Yes, massively so." But then, I would take it in a totally different direction. To me, the complexity of bioinformatics come from the biology. How do you think about weird biological edge cases? What do your distributions look like and how do you choose thresholds? How do you even form a good question?

Thinks like [B|S|Cr]am files are complex in their own way, but mostly they're just kinda annoying to have to figure out. You can dig in as deep as you need pretty easily.

On the other hand, maybe I'm over-simplifying because I feel more comfortable in this domain, which I think is your point.

Oh, interesting. I just wrote a reply saying the exact opposite. I remember learning scientific computing as being much less frustrating. Sometimes you'd have some error spawning out of some ancient C/Fortran library. But that was rare for me. Even after a couple of years on the web, I still feel like I encounter issues where I just don't even know how to start.

You're absolutely right. Webdev is certainly its own fully fleshed out fields. Oddly, I think I can play off your facetious quote and turn it into a more analytical way of framing what the post was about.

"I am a biochem major but I decided to work in bioinformatics/scientific-programming despite having minimal skills or experience and I ran into loads of problems and issues that I was able to steadily solve because the ecosystem felt sane, the tracebacks were clear, and the debugging usually had a clear path forward. Then I was a bioinformatics professional doing work in webdev [...] I ran into loads of problems [...] that felt consistently more opaque and magical than when I was learning scientific programming"

I think that's the heart of it. The transition to the web feels so much more chaotic than the transition to bioinformatics.

Two quick points here:

1. A few years ago, I probably would have made the mistake of actually hard-coding my connection strings, usernames and passwords. I'm pretty sure I did that on my first ever webapp, cause I didn't know any better. So, not defending my intelligence, or taking any offense at your statement. 2. But... That's not what's happened here. I'm setting the redis url inside Heroku's "Config Vars" section, and then reading it in with Django's `env()` functionality, as is appropriate. But the url has seemingly been changed from underneath me, for a reason I still don't fully understand.

Side-note: I used to be under the impression that CS was "harder" than biology, and that anyone who understood CS could pick up biology at will, if they decided. Turns out that's not the case, haha.

This is a fantastic point. Payments in particular have been intimidating for me. Nobody wants to pay for something and then have some goofy mistake on the backend mess up processing it. Or even worse, make them feel like their credit card is susceptible to theft.

I don't know how to explain it, exactly, but worrying about this definitely made development more difficult, even when initially setting up and testing out.

Django has been a joy to work with. As other's have mentioned, I'm a huge fan of their documentation. I think they do a great job of letting you quickly hop between Tutorial and Reference docs. Lots of links help me quickly dive into more detail when I need, then jump back out.

> JS is forced everywhere

I think this has a lot to do with it, interestingly. The web has become so ubiquitous, and the major players are so resourced, that the barrier to entry can seem really high. Maybe I'm wrong, but my perception is that potential customers wouldn't take a second glance at my sight if it were plain html with minimal CSS and didn't render perfectly on mobile.

> I am glad I don't do web GUIs

Same.

I heard there's a great new site that can help you learn about bio if you're interested... You know, if the site will let you login, that is. ;)

As my PI used to say, "If it were easy, it wouldn't be fun. And we wouldn't have jobs."

Oh no! It's github pages and totally static, so it should recover pretty easily, I hope. Thanks for the archive though!

It's kind of ironic. While I've been thinking about the complexity of software/webdev for a while, I was feeling a little unsure about posting this particular link because I wrote it in a hasty, semi-embittered fit of annoyance. Regardless, thanks for the read. :)

This has been my first experience with it and it seems like a great tool to ensure structured thinking. It's easy to give up a level or two deep and just say, "Oh, it's probably because..."

Hey everyone! I’m excited to introduce CodeStories, an education platform for professionals, as well as our first publicly available course, Intermediate Python for Bioinformatics (InPyBio)!

The purpose of InPyBio is to empower all life scientists to analyze and understand their own data. There's a lot more I wanted to say about both CodeStories and InPyBio, but I couldn't fit it in the character limit. I've written it up here instead: https://mycodestories.com/about/#our_story

I’m going to be monitoring the thread for the next few hours, so please feel free to leave any comments or questions you have. I’m looking forward to seeing what you all think and potentially meeting some of you soon!

Note: I'm not affiliated with Insight in any way.

I'd be interested to hear what people think about:

1. Income Share Agreements in general

2. The messaging around this price increase (from $0 to ~$18,000) premised on funding a new feature/experience. Why not just say that they need to charge for the program?

This is pretty cool. Anyone have thoughts as to _why_ they’re making this move?

> you may want to start off by scraping all the profile pages instead

Oddly enough, I'm in the middle of this project right now! There are over 600,000 users, and it turns out that many of them use their profiles to share links to things other than personal blogs. I've done some scripting to automate deciding if a link is a personal site or not, but the whole endeavor has been significantly less trivial than I had hoped.

Regardless, I plan on sharing results soon, so be on the lookout!

What are some examples of communities that are significantly "healthier" than HN?

I'm particularly curious about communities that are "similar" to HN. Use whatever definitions of "healthier" and "similar" you think are appropriate.

I love jupyter notebooks. Without them, I wouldn’t have been half as productive as I was during my PhD.

Here’s a post I wrote just a few weeks ago describing some of the conventions that I established for myself over the course of 5 years:

https://jessimekirk.com/blog/notebook_rules/

I suspect that a lot of the conventions I describe help mitigate problems described here, some of which should be strictly or optionally enforced by the notebook instead of the user.

(The site’s very much a work in progress, so expect to see odd and broken things if you go poking around.)

Yea, I would second this.

I've always enjoyed Heroku, but feel like I'm paying a premium because I don't know enough to do "real" cloud work.

"If I were a more experienced developer, I could run this on AWS for pennies on the dollar".

Honestly, I don't know where that sentiment comes from exactly. It's at least partially coupled with the fact that all of add-ons you would need to pay for to run a small business site add up pretty quickly, from what I can tell.

“Clinical Exome Studies Have Inconsistent Coverage” seems like a significantly better title. The current HN one doesn’t make sense.

Incidentally, this is also one of the main points of “21 Lessons for the 21st Century” by Yuval Noah Harari. His argument is that human’s morality is built for interacting with a small tribe of people. You know where your moccasins come from, because the person who made them sleeps at the fire next to yours.

> Time to break out the champagne!

This was a lot of fun; I'd definitely play level 2.

The nice thing about it was that you had some flexibility around getting the exact SQL query, and just visualizing a slightly larger superset of the data.

I’m surprised nobody has mentioned AppHarvest yet. The NYT[1] recently covered them.

Their investor list in and of itself is pretty interesting.

Plus, their building out of Morehead, Ky. Morehead was the “big city” when I was growing up, so it’s cool to see innovation there.

[1] https://www.nytimes.com/2019/09/03/business/appharvest-green...

#2, and this comment in general, is a great point.

I recently wrote my first piece of productivity software, which I use everyday. The main benefit I get out of it is reminding myself, “This structure is how I want to think about things.”

The unlimited freedom of a spreadsheet comes with downsides, at least for me.

I find myself on Chris' site all the time

https://chrisalbon.com/

Another +1 for sentry. I used it (basically accidentally) for a year because it's part of the cookiecutter-django framework[1]. I don't think there was a single issue with it the whole time we used it.

[1] https://github.com/pydanny/cookiecutter-django

Multiple good points here! I should have said “useful in a year without context.” or something similar. The daily write-ups will always be directly available from the aggregated summaries. But pictures are another great way of providing context! Maybe it’s because I’m more of a backend person, but I haven’t felt a pressing need to add screenshots at work yet. All of the scenarios you suggested though make it sound like a great idea. Thanks!

Both, I suppose. The app is far enough along that I’m using it myself (for work and the project), but it’s still messy and I’m iterating on it. An “Export data” is on my TODO, but not done yet, so the notes are currently trapped.