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Tiny Python Projects

by Ken Youens-Clark

The book of the week from 26 Apr 2021 to 30 Apr 2021

A long journey is really a lot of little steps. The same is true when you’re learning Python, so you may as well have some fun along the way! Written in a lighthearted style with entertaining exercises that build powerful skills, Tiny Python Projects takes you from amateur to Pythonista as you create 22 bitesize programs. Each tiny project teaches you a new programming concept, from the basics of lists and strings right through to regular expressions and randomness. Along the way you’ll also discover how testing can make you a better programmer in any language.

Questions and Answers

Dustin Coates

Hi Ken Youens-Clark, great to see a fellow Manning author! Would you say your book is a good fit for someone coming from other languages? I’ve a lot of experience with JS and Ruby, for example, but most of my Python is written with a JS accent. Would your book be good to learn the Python way of doing things?

Ken Youens-Clark

Hey, Dustin. Yes, I specifically hope that someone is coming from a previous language, but I also try to cover everything just in case this is a person’s first Python book. I try to show Pythonic ways to do things you might know from other languages, but I also try to show that Python is quite flexible and often has many ways to accomplish the same task. For instance, the list comprehension is very Pythonic (it’s similar to Haskell in this way). C-type languages such as JavaScript might initialize an empty list and use a for loop to build it up
>>> powers_of_two = [] >>> for i in range(4): ... powers_of_two.append(2**i) ... >>> powers_of_two [1, 2, 4, 8]
But a list comprehension can do this in one step:
>>> powers_of_two = [2**i for i in range(4)] >>> powers_of_two [1, 2, 4, 8]
I think these kinds of idioms make Python easier to read and share.

Ken Youens-Clark

I should say that I quite flagrantly violate the Python Zen of “there should be one obvious way to do something.” I specifically show many ways to accomplish the same ideas, and I really like to get the reader used to purely functional ideas. So, if you can see how a for loop (which is a statement that produces no result) can be written as a list comprehension (which is an expression that returns a value), then you might be comfortable writing this with map:
>>> list(map(lambda i: 2**i, range(4))) [1, 2, 4, 8]
Similarly, if you are comfortable using a list comprehension with a guard to conditionally accept some values:
>>> evens = [n for n in range(10) if n % 2 == 0] >>> evens [0, 2, 4, 6, 8]
Then you might be good with learning to use filter:
>>> list(filter(lambda n: n % 2 == 0, range(10))) [0, 2, 4, 6, 8]
JavaScript really uses functions in a similar way, in my experience. That is, functions are first-class objects that can be passed as values and overwritten, used as callbacks, etc. I think teaching these kinds of ideas to novice programmers will make it easier for them to launch into other languages, too.

Eric Sims

Wow, those examples are really helpful. I am getting better at using list comprehensions, but that filter with the lambda function to do the same thing is cool!

Ken Youens-Clark

When you start thinking in terms of functions and how they fit together, you can see how to fit code together like Lego pieces. Working in a strongly/statically typed, purely functional language (e.g., Haskell or Elm) is one way to burn your boats and force yourself to think this way. My experience in Elm totally changed my approach to using imperative, dynamically typed languages.

Ken Youens-Clark

Note that you don’t have to write lambda defs. You can also use regular functions:
>>> def p2(n): return 2**n ... >>> list(map(p2, range(4))) [1, 2, 4, 8]

Brian Fleming

Hi Ken Youens-Clark
Can you recommend whether you think a Marketing Analyst (GA/SQL based) that’s looking to upgrade their skills would be better starting with something like your book and Python or concentrate on a new platform and deprioritise coding/Python?

Ken Youens-Clark

SQL databases have been an integral part of everything I’ve written over the last 25 years. For the longest time, I relied on Perl for this, but Python’s integration with SQL platforms is really great. For instance, I now mostly use Postgres and rely on the peewee module to create an object-relational module (ORM) that minimizes the amount of raw SQL I write. When I combine that with something like FastAPI and type hints, I can bang out a web back-end API in relatively.
For instance, I’m currently working on ct.c-path.org for my employer (The Critical Path Institute). This a mirror of clinicaltrials.gov with a custom query interface. All my code is in https://github.com/criticalpathinstitute/ctweb, and you can look in the “fastapi” directory to see how I leverage these technologies to create what is, IMHO, a readable codebase for interacting with Postgres.
So, TL;DR: Yes, I would definitely recommend learning Python and how to integrate with databases. If you combine types and tests, then I think you’ll get even more out of this, and I discuss these at length in my book(s).

Brian Fleming

Thanks Ken, I’ll have a look at the repo 🙂

Ken Youens-Clark

I have plans to pitch a book about Python + ORMs + SQL databases (SQLite, Postgres) one day. My current project is Hands-on Systems Programming with Rust for O’Reilly, and I might pitch a book on purely functional programming with Elm next. Not sure when I’ll get to Python/SQL.

Matthew Emerick

Hey, Ken Youens-Clark! Thanks for doing this.
Do your tiny projects make for a great portfolio strictly as they are in the book? Are there recommendations to expand them?

Ken Youens-Clark

If I were a potential employer and saw that someone had managed to create a repository of programs that included documentation, sample data, and tested code, I’d be fairly impressed. If a person did nothing other than type out the code I present and run the tests, I think that would be a fairly impressive first step in learning how to organize, run, and test Python. If they had managed to write their own solutions before consulting my versions, that would be even more impressive. If they went on to expand the programs by adding features and tests, that would be <chef’s kiss>. Each chapter has a “Going Further” list of suggested expansions, but one’s imagination is the limit.

Matthew Emerick

Do the projects put together teach a wide enough variety of skills to give a deeper understanding of what Python is capable of?

Ken Youens-Clark

Python can do an incredible amount, but I can only move the user a couple clicks along. That is, when I first started talking with Manning, they suggested I imagine a scale 1-10 where 1 is a beginner and 10 is an expert. I can only hope to move, say, a 2-3 level user to maybe a 5-6. Trying to move someone from a 2 to a 9 in one book makes for material that moves too quickly. So I try very hard to make a novice programmer feel comfortable with testing which in and of itself is usually considered some sort of super-skill. Testing is not actually all that difficult, but I hardly find anyone trying to teach this vitally important skill. While I try to show just how flexible Python is as a language, I would say my secret goal is to get people to think about how to write small, testable, composable functions. I want my readers to be able to take these skills and apply them to learning and writing any other languages they encounter.

Matthew Emerick

Is there a project in your book that shows you how to call C code?

Ken Youens-Clark

No, I would consider that a very advanced skill. To be honest, I’ve never written a C program beyond “Hello, world!” I never have need for C, and I have no idea how to call it from Python. My next book is a similar beginner’s guide to Rust, which I would consider a much better language for trying to interface with external libraries.

Sara Garcia

Hi Ken Youens-Clark
I’m reading the list of the Python projects of your book and I wonder if the reader should have a previous knowledge of python, or any other programming language or concepts. I also want to know what concepts do you recommend to expand, and if you have another book to recommend for that.

Ken Youens-Clark

Hi, Sara. I honestly think Tiny Python Projects is a great 2nd or 3rd Python book. If you don’t know the language at all, you might find The Quick Python Book or something like that a good introduction. If you know any other language at all, my book is probably a fast way to get familiar with the language. Just reading about concepts is not at all the same as trying to write your own programs. Writing forces you to really interact with the language, and learning how to test your programs will really focus your attention.
I think my book explains a lot of basic programming concepts reasonably well, things like loops and variables and functions. I completely avoid object-oriented programming for various reasons I could explain if you care. If you don’t known OOP, then you definitely don’t need that concept. I subtly push my own biases that include a penchant for purely functional program, immutable data structures (e.g., tuples), the use of testing, and the introduction of type hints which comes in the last chapter. If you like these ideas, you might be interested in my second book, Mastering Python for Bioinformatics (O’Reilly) which will be in print next month. That book goes much deeper into testing, types, and functions, even if you are necessarily interested in biology + computer science. The material is actually fascinating, and the solutions can get quite complex.

Anna Parfenova

Hi Ken Youens-Clark!
Despite I don’t belong to Z-generation, it’s hard for me to start learning (programming) from books, when there are plenty of video-courses and other web-resources available.
I see one big pro of book:

  • it will make me re-type things instead of copy-pasting.
    What are other pros (and maybe cons)?
Alexey Grigorev

Actually, you can copy-paste from pdf…

Ken Youens-Clark

The reader will gain the biggest benefit by writing the programs. Even if you do copy-and-paste from the PDF, the act of getting the code, altering the programs, and running the tests will give you a categorically different experience from simply reading the book. I strongly encourage the reader to type in all the examples, both the examples in the REPL and the actual programs. In the language of pedagogy, this is an “active learning” approach where the student does stuff rather than just listens or reads. I really enjoyed my times in the classroom using these kinds of exercises to get people writing and testing programs. Those classes were so different from times when I would just lecture about Python lists and blah blah blah. If you want to learn to write programs, you have to write programs!

Ken Youens-Clark

Oh, also all the code/tests/solutions are directly available from my GitHub repo at https://github.com/kyclark/tiny_python_projects.

Ken Youens-Clark

And I’ve also created videos to walk a person through the solutions, step-by-step. You can find them all from http://tinypythonprojects.com/. This is another important skill I’m trying to teach–that is, how should one start a program, what’s the next logical step. For instance, I suggest using the bin/new.py program in the repo, then defining the parameters using argparse and testing the interface with the first couple tests. Then move to maybe printing something, maybe reading a file, etc. The process of writing and testing is much more important than just learning Python syntax.

Vladimir Finkelshtein

In my personal experience, online videos tend to be on the shorter side, so they will usually cover each topic in much less detail than a corresponding chapter in a decent book. Many of these videos are made by reading a chapter from a good book and trying to squeeze it into a determined time interval.

Anna Parfenova

Thank you, Ken Youens-Clark 🙏
Good point, Vladimir Finkelshtein 🤔

Eric Sims

Not so much a question at the moment, but a comment from the GitHub repo: I really like your philosophy of “test-driven development” and writing tests before writing code. Taking the time to define success before jumping into a project would probably save me a fair bit of time and certainly help manage scope creep! 😄

Ken Youens-Clark

“Weeks of coding can save you hours of planning.” – Anonymous

Ken Youens-Clark

I really feel that TDD is an under-appreciated teaching tool. I found that giving my students a test suite makes it crystal clear what the expectations are for a program. I would actually see students get excited when they would go from all failing tests to passing one or two tests and finally passing all tests. The motivation of see all those passes should not be dismissed.

Eric Sims

I hadn’t thought of it that way, but you are definitely right. It feels so rewarding to solve lots of small problems along the way and celebrate the small wins.

Ken Youens-Clark

Tests really prove their value when you try to add a new feature to your program and find you’ve accidentally broken something that used to work.

Simon Steinkamp

I had a quick look over the projects and the Github Repro and it sure looks interesting 🙂
As someone who has done quite some coding in Python so far (including a little package with tests) but never took the time to get a formal / solid Python foundation - I was wondering what someone like me could get out of your book and whether it could help to get more structure in the hacky coding style? ( I hope the phrasing isn’t to confusing)

Ken Youens-Clark

If you are a more experienced developer, the first few chapters may feel a little simple for you. I’d still encourage you to work through even the most basic programs to get a feel for using tests to verify your programs. TDD encourages us to first write tests and watch them fail. Then fix the code until the tests pass. If you’ve never done this before, you may be surprised at just how easy testing with a framework like pytest can be. I really feel like “testing” is made out to be some really advanced topic, beyond the comprehension of students and novices, and is something you’ll learn about on the job. My experience is that testing is easier than not, and that not enough people on the job use testing or ever teach it. I may also surprise you with how differently Python can be written when you rely mostly on functions and tests. For instance, if you’ve mostly done OO-style programming with Python, you’ll see much simpler code in my examples. So, yes, I think you’d get a good bit from going through my examples.

Simon Steinkamp

Great! Thanks 🙂

Gant

Hi Ken Youens-Clark what is the most fun project in the book?

Ken Youens-Clark

T’ehres stenhoimg aoubt The Srebalcmr taht I find rellay fun. I’ts amnizag taht your biarn can raed this text, and I ejnoy wtrinig pgmraros taht eplmoy rodnamsnes. (https://github.com/kyclark/tiny_python_projects/tree/master/16_scrambler)

Ken Youens-Clark

I also love ideas about encryption, and Gematria is interesting to me. I got that idea while reading The Chosen by Chaim Potok.

Ken Youens-Clark

Although this is not a reversible encryption. My latest book using Rust will likely include a simple ROT13 (rotate 13 characters) encryptor.

Ken Youens-Clark

Each chapter is intended to teach some few skills. Even though they are playful, trivial programs like “Apples and Bananas” can lead you to explore many interesting ways to write the same idea (https://github.com/kyclark/tiny_python_projects/tree/master/08_apples_and_bananas) while testing helps you learn how to refactor programs while still ensuring they work.

Glenn

Hi Ken, what’s something about Python that you learned while writing this book that you didn’t know about beforehand? And possibly the most important question, in terms of “RegEx”, are you of the camp that it’s pronounced with a hard g (like garden) or soft g (like generator)?

Ken Youens-Clark

Hi, Glenn. Your first question is really interesting. I actually find it remarkable that I got a chance to write a book on Python when I’d only been working in the language a couple of years. I spent most of my career using Perl, which I find to be extremely similar in all the important ways (dynamically typed, c-like syntax, modules, variables). Still, there were lots of nuances to learn, and I’d say that I got much more familiar with testing/pytest and the use of randomness which I’d never really used much before. E.g., while writing one of the exercises I discovered that the reader might make some random choices in a different order than I did and so would end up with a different answer. Not a wrong answer, just different because the RNG (random number generator) would be called differently. I learned much more about testing writing this second book (Mastering Python for Bioinformatics, O’Reilly, 2021) such as how to better organize tests and data as well as how to integrate linting and type checking.
As to your second question, I guess I’m completely inconsistent because I pronounce “regex” with a soft g like “rej-ex” but “regular” has a hard g. Completely random anecdote: A couple of years ago I was walking across the Univ of AZ campus to get a coffee with a friend and we bumped into Noam Chomsky (who’s done tons of work in linguistics and “regular” languages and such). We were star-struck.

Glenn

Thanks for the response, and a very cool story about Noam Chomsky! I remember seeing Perl listed on a Stack Overflow survey as the “most hated language” by programmers. What are your thoughts on that?

Ken Youens-Clark

It’s easy to write bad code in any language. Perl’s penchant for sigils like @{ $hash{ $key }} can be really hard to read. I understand that fine, but I also appreciate that it’s hard to read. Perl was ascendent in the late 90s and early aughts when I became a web developer and fell into bioinformatics. Perl was king of text processing and regular expressions, and it worked really well in those domains. I loved it very much and only used Perl for about 15 years. I released a few modules (https://metacpan.org/author/KCLARK), SQL::Translator was perhaps one of my best works, and I built and maintained a cool genomic map viewer (https://pubmed.ncbi.nlm.nih.gov/19648141/).
Sometime in the last 10 year, Python simply took over scientific computing. Modules like Numpy, Pandas, and Scikit-learn are just too good and important to ignore. In web development, I found Perl modules I’d used for so long couldn’t compare with the features I found in JavaScript and Python. It was teaching that pushed me over the edge, though. I asked my boss at UA to move our intro programming from Perl to Python because I thought it was much easier to teach and we were doing a disservice by teaching students an older language when Python was clearly more in demand. Perl still has a special place in my heart, but I’ve moved on. I thought Perl 6/Raku was interesting, but I’m not sure it’s ever going to draw me in. My biggest push lately has been into using Elm for web front-ends and Rust for systems programs, and, in fact, my next book with O’Reilly is an intro to Rust.

Glenn

Thanks for the detailed response, Ken! My first language was JavaScript and have worked on teams that have used Go, Swift, and Python. I found that Python was the quickest to learn and be productive in (but could also be because I started working with it after years of programming experience). I’m still fairly new to it, but blown away by pandas and scikit-learn. Sounds like you’re busy writing a lot of books!!

Jeffrey Jex

Hi Ken, with the idea of working on fun projects and puzzles, what minimum age range would this book be appropriate for? I saw you mentioned it’s a great 2nd or 3rd python book in an earlier comment. In other words, would this work for early teenagers still learning to code?

Ken Youens-Clark

I wrote this material when I was teaching college-aged beginners while I was working at the Univ of AZ, but I had in mind at least high-school aged readers and perhaps even younger. I illustrated it with my crude cartoons and tried to interject enough levity so it doesn’t feel like a textbook. The material is drawn from simple games that kids would likely know like “Telephone” and “Mad Libs” so I can focus on learning syntax and testing more than anything else. I would love to think that teenagers would find this approachable, but I don’t have direct experience with students younger than 18 or so.

Jeffrey Jex

👍 thanks for the info!

Tatyjana Ankudo

Hi Ken! Thanks for your work. How is this book different from another Python books? What particular did you pay the most attention to writing the book?

Ken Youens-Clark

I think it took me writing the book to finally realize that the biggest difference is that I’m trying to teach people how and why to test their code. There are so many beginner Python books that just snippets of code like how to implement something like a Caesar cipher, which is cool, but they don’t show how to integrate this into a complete program that, for instance, takes a text file as an argument, validates said file, reads it, encrypts it, and writes the output perhaps to STDOUT or maybe to another file. Along the way, how do you test the program to ensure it does all those things correctly? And how does one go about writing such a complicated program? I think it’s not actually too difficult to teach all these concepts to novice programmers. It’s actually better to set the bar a little higher and let new programmers know that we’re expected to write programs that have documentation and tests, that it’s incumbent on the author to provide good code to users. But I try to make all this subtext. The foreground is solving little puzzles and these other things are techniques that help one do that. When the reader has finished the book, though, they’ve seen dozens of unit and integration tests and have used their own interfaces to run their programs. I think this is the most important thing my readers could learn and definitely these are skills I don’t see other authors attempting to teach.

Ken Youens-Clark

Sorry to go on and on, but I love this quote about testing:
More than the act of testing, the act of designing tests is one of the best bug preventers
known. The thinking that must be done to create a useful test can discover and eliminate
bugs before they are coded—indeed, test-design thinking can discover and eliminate
bugs at every stage in the creation of software, from conception to specification, to
design, coding, and the rest.
—Boris Beizer, Software Testing Techniques

Tatyjana Ankudo

I am glad you wrote this book, because I absolutely agree to your point of view. I was lucky to get very good mentor who make me love testing. Your book is in my list “must read”

Alexey Grigorev

Were there some tiny projects that you wanted to include, but couldn’t?

Ken Youens-Clark

I was only able to include about 1/3-1/2 of the exercises I originally sketched out. That being my first book, I had no idea of the exposition I would end up writing. For some reason, I originally thought I would spend just a few pages per exercise and let the code speak for itself. I came to realize this wasn’t really teaching, and so I had to create much more prose. I put a bunch of other ideas into https://github.com/kyclark/more_tiny_python_projects some of which might one day find their way into a more advanced Python programming book, one that would advocate more for the use of types which I do in my bioinformatics book. I’m surprised that types seem to be rejected by a lot of very accomplished Python programmers, so this might be a somewhat controversial stance. I’m also very interested to see how the latest language features of 3.10 and beyond evolve, e.g., pattern matching (which is not the same as regexes) and switch/case statements could really improve Python code. If I write another Python book, I will definitely push to show how these features would look.

Alexey Grigorev

That’s a very familiar story. thanks for sharing!

Alexey Grigorev

Also, for someone who’s learning some other programming language (say Rust), would you recommend the same set of tiny projects or something else?

Ken Youens-Clark

Absolutely! In fact, to become a better programmer in general I would strongly advocate to try writing these ideas in any other language you know. Try JavaScript or C. Then go make yourself learn something completely different like Haskell or Lisp. Certainly Rust is an interesting choice, too. My next book project is “beginner” programs in Rust, but the level of that beginner is expected to be a bit further along in their career than for TPP, so the programs are more complex.

Ken Youens-Clark

For example, the first Rust project in my book is an implementation of echo which repeats back anything it is given. This is essentially “Hello, world” and is very close to the Crow’s Nest exercise in TPP. I have Tic-Tac-Toe in TPP, and I might include Hangman in my Rust book (depending on space). Both are simple games that iterate through play and maintain state. TPP has text transformations like The Scrambler, Gematria, and Jump The Five, and my Rust book will likely include encoders for ROT13 (rotate characters 13 so A becomes M, etc.) and a Pig Latin (“ig-pay atlin-lay”). The TPP Workout-of-the-Day (WOD) shows how to read a CSV file, and in Rust I’m writing a version of cut that also handles delimited text.

Ken Youens-Clark

The goal is to get the reader to see patterns. I mostly see the world now in terms of primitives like strings and numbers and then data structures like lists, sets, and dictionaries. Functions transform these in various ways, so it’s mostly a matter of hooking up the plumbing correctly, no matter the language. Some languages are stricter in the compile phase so they help you find places where you didn’t get it right. Rust won’t even budge until it’s satisfied that everything is perfect, whereas Python will just blow up at runtime so it’s important to include types and tests.

Alexey Grigorev

Thanks!
Just curious, why would you recommend learning lisp or haskell? Just because they are quite different from the mainsteam imperative languages?

Alexey Grigorev

I also know that you’re quite a prolific author. How do you manage to finish one book and find the energy to jump on another one immediately?

Ken Youens-Clark

I’m not sure I’d call myself prolific just yet. My second book, Mastering Python for Bioinformatics (O’Reilly) is heading to press next week, and I have started my third on Rust. Maybe if I get to five books I’ll accept that description! I’ve been programming for about 25 years and spent a good bit of time teaching and mentoring and reviewing code. I finally found enough to say, and now I feel like I just need to write and write to get all these ideas down on paper.

Ken Youens-Clark

I recall when I started my undergraduate degree at the Univ of North Texas back in 1990. I signed on to be a Jazz Studies major because I wanted to study the drum set. I’d be playing since age 9, and the choices were either to study music ed to become an instructor, music performance to become an orchestral player, or Jazz to study the kit. Anyway, it seems ridiculous now that I was studying Jazz because I’d never listened to it in my life.

Ken Youens-Clark

I could barely read music, couldn’t hear the difference b/w a major and minor scale, couldn’t vocalize, didn’t know jack about music history or theory. Mostly I could bang out some rock beats on a kit, and yet I was going to study music! Anyway, I come to quickly realize that I’m in way over my head. I’m trying to learn how to play swing on the kit when I’ve mostly just listened to hard rock. It was a radical change. I had no vocabulary.

Ken Youens-Clark

Every member of a jazz group is expected to be a virtuoso and take a solo. You have to know the form of a tune, play in the correct style, interact in real time with other players. When it came time to take a solo, I would just freeze. I had no idea what to “say” on my instrument.

Ken Youens-Clark

One of the instructors patiently said one day that jazz is something of an old person’s music. That it takes a really long time, lots of studying and playing and listening, to find something to say on your instrument, particularly something new.

Ken Youens-Clark

Until then, we should just study what others have said, mimic them, write down ideas, synthesize until we found our own voices. This would ultimately take decades, so don’t be in too much of a hurry.

Ken Youens-Clark

After a couple of years, I switched majors (a few times), but I kept studying music on my own. I got deeper into literature and reading and thought about writing fiction, but, again, this was so beyond me. I still harbor delusions of writing stories. The words of my jazz prof stuck with me, though. It would take a really long time for me to find something to say, so I’ve just kept trying over the years to work out what I have to bring.

Ken Youens-Clark

I also really thought about teaching as a career, but obviously programming pays way better. While working at the Univ of AZ, I finally got a chance to teach in a classroom by helping my boss, Dr. Bonnie Hurwitz. At first we split classes, her teaching science (metagenomics) and me programming so our student could learn how to do computational research.

Ken Youens-Clark

Teaching was a huge challenge, and I really sucked at it at first. I would type out my lectures entirely long-hand, that is, as a prose document to work out what I wanted to say in an hour. That’s pretty much the length of a decent chapter. I would devise examples and sequence things to show, for instance, what is a list, why it’s useful, how to manipulate it, where you’ll find one in the wild.

Ken Youens-Clark

After a couple of years, I finally designed an entire course just on the programming material and got to teach for entire semesters. That was really life-changing. I enjoyed working with students and seeing their struggles. Since I learned to program so long ago, it was easy to forget what was hard to learn. I kept refining my examples and prose and lectures and moved entirely towards live-coding in class.

Ken Youens-Clark

“Active learning” is a great way to keep people from falling asleep in class and really helps people retain information. So I have adopted this active approach to writing. I describe a challenge, give the reader some information and hints on how to solve it along with the data and tests to know when things are correct, and push the reader to work it out. Then I present some different ways to solve the problem.

Ken Youens-Clark

I don’t know if it’s just a formula I’m following for now. I’m not trying to be derivative, but this is the format for TPP, the bioinformatics book, and now the Rust book. There are plenty of other books that describe everything you want to know about a list or a dictionary for a given language, but not enough that show you when and how to use one in an actual program.

Ken Youens-Clark

As for the energy, I’ve got issues. I feel really OCD about writing at this point in my life. Like I’ve been trying to learn to speak and finally figured it out. My father died young, and I think I’m haunted by ideas of mortality. I recently watched (and rewatched and rewatched many times) “Hamilton” with my daughter, so I guess “I am not throwing away my shot.”

Ken Youens-Clark

Sorry if that took a weird turn, but you hit a button, I guess.

Alexey Grigorev

What I can see is you definitely love writing 😅

Alexey Grigorev

I was really curious where the jazz story is leading!

Alexey Grigorev

So, if I can attempt to summarize it, you did a lot of work prior to writing the book, and already had experience with structuring your thoughts on paper. Am I close?

Alexey Grigorev

I also like the idea of active learning! That’s really great! I haven’t heard this term (in this context) previously

Ken Youens-Clark

Yes, you summarized it fine. I started to scratch the surface of learning formal pedagogy when I was working on my MS at UA. I may have an opportunity to teach there this fall, and I’d love to continue learning more about the science and art of teaching. As interesting as I think my own lectures are, I’ve literally seen my students struggling to stay awake. That doesn’t happen when everyone is trying to write code together. Sometime I have them do pair programming in class, too. Another great teaching tool.

Alexey Grigorev

Okay, I have a few more questions!
You just finished a book about bioinformatics. Can you tell us a bit what bioinformatics is and what kind of problems it solves?

Ken Youens-Clark

Yes, my latest book is with O’Reilly and is called Mastering Python for Bioinformatics (https://learning.oreilly.com/library/view/mastering-python-for/9781098100872/). Bioinformatics is the application of computer science to biology. There was a time up until the 1990s when most biological data sets would easily fit into small Excel files. With the advent of genome sequencing, that is no longer the case. Sequencers have been able to create more and more data for cheaper and cheaper prices at a rate that outpaces Moore’s law. Biology is swimming in data, and so it’s imperative to use computer science to find patterns.

Ken Youens-Clark

In French, “informatics” is computer science, so it makes a little more sense. Anyway, I’ve been working in and around bioinformatics since 2001 when I got a job as a web developer in the lab of Dr. Lincoln Stein at Cold Spring Harbor Labs. He was a big Perl name, author of core modules and several books. Hanging around him at conferences was like being around a rock star back then. It was weird.

Ken Youens-Clark

I knew basically nothing about biology. My undergrad degree was English lit (minor in music) I was hired to build databases and code Perl web interfaces. I also wrote a comparative map viewer that many people used for a while (https://pubmed.ncbi.nlm.nih.gov/19648141/) but I never felt I had my bona fides in the field. I jumped at the chance to work at the Univ of AZ as I wanted to earn my MS which I finished in 2019. That gave the me chance to fill in a lot of missing knowledge esp in stats and machine learning.

Ken Youens-Clark

When I was writing material to teach basic programming at UA, I started with the ideas in Tiny Python Projects, and then showed how those simple ideas had cognates in biology. I had dozens of ideas for chapters for a book on bioinformatics, but I realized that the Rosalind.info problems just couldn’t be topped.

Ken Youens-Clark

So I chose 14 of those challenges and showed how to solve them in Python, ordering them in such a way to build on the ideas as in TPP. Then I threw in 5 more of my own ideas to show some more advanced programs.

Ken Youens-Clark

I haven’t quite answered your question – What does bioinformatics solve? Well, pretty much all the big advances in biology including things like the COVID vaccine are due to using computational approaches to solving data problems. For instance, protein folding is a wicked hard problem, but all the information to figure out the 3D structure of a protein is necessarily contained in the raw DNA sequence. We just have to figure out how to go from one to the other.

Ken Youens-Clark

I worked for 13 years on a plant genomics project where we looked at things like orthologous genes, that is genes that basically encode the same proteins/function in different plants. For instance, some species of rice are more drought tolerant than others. Why? Is it one gene or a set of genes? Can those be transferred to another species? Humans have been doing gene transfers for centuries in plants and animals through selective breeding. Now we are able to select individual genes.

Ken Youens-Clark

Then I worked in metagenomics at UA which is the study of uncultured genomes found in the wild. Think about taking a sample of ocean water and trying to figure out all the microbial species living in it by extracting the DNA and sequencing everything. We only know a fraction of the species existing on earth, so a lot of the DNA you find will be unidentifiable. Still, you can find genic regions and compare them to known genes/structures to infer what’s going on the organisms that are present. Extend that to a sample from a person with an unknown infection. Take a sample maybe from the gut. Do they have C. difficile or something else like a virus? Antibiotics don’t work on viruses, so antibiotics could actually make the patient sicker. If someone is septic, you give the worst antibiotic possible but you need to de-escalate quickly so you need to identify what organisms are present to choose the right antibiotic (or something else entirely).

Ken Youens-Clark

The field of bioinformatics is huge and growing, e.g., biotech. It’s an exciting field.

Alexey Grigorev

And why did you decide to write a book about it?

Alexey Grigorev

Is it something you do at work?

Ken Youens-Clark

Oh, I should have answered that here, but yes, most of what I’ve done over the last 20 years.

Wendy Mak

to add to the above questions above bioinformatics– I find it quite an interesting topic, but as someone who has no biology background beyond high school, what’s a good way to learn about it/get involved in projects etc? would you say your new book a good starting point?

Ken Youens-Clark

I had no formal training when I started, but I was also not hired to do bioinformatics per se but web development. If you are truly interested, a formal training would be pretty necessary. Many people in the field have PhDs or at least an MS. There are some degree programs in bioinformatics, but usually people train in something like molecular biology or biochemistry and do lots of coding. Some people formally train in both biology and CS, and those people usually have it really going on.

Ken Youens-Clark

If you wanted to test the waters, you might try working through the exercises in my new book (Rosalind.info and then continue on with others from <http://Rosalind.info). The book Bioinformatics Algorithms is also great. Compeau wrote that and Rosalind!

Ken Youens-Clark

Most people in the field are biologist who learn to code or coders who learn biology. If you know one really well, it might be possible to get in with a lab. That’s how I started, as a coder who learned biology, but wow does the biology get HEAVY really quickly.

Ken Youens-Clark

There are a few rare people like Lincoln Stein who really get both the CS and the biology. FWIW, he’s at the Ontario Inst for Cancer Research now. He’s just killing it. A lot of PIs (principal investigators, the people who run the labs, write the grants, spend the money) in my experience are mostly very good biologists who have research questions but don’t have the time to write all the code. I think a hotshot programmer who’s willing to really learn a lot of biology could get hired.

Ken Youens-Clark

Someone with a deep background in biology who’s also a good coder might choose to go to work for a biotech firm like 10X Genomics or they might start their own lab.

Ken Youens-Clark

But look over the job postings at 10X and you’ll see they aren’t exclusively looking for biology people. They also need QA/testers and front-end devs and cloud computing specialists and workflow developers.

Ken Youens-Clark

It’s a big field, and often you’ll find there are projects that are really contributing to the good of mankind. Even though Big Pharma can do bad things, where would we be without the COVID vaccines?!

Saulius Lukauskas

I currently work in the field so can add a bit as well if the author doesn’t mind me hijacking this thread. Bioinformatics in the classical sense is slowly disappearing as a field of its own as it is getting absorbed by data science: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001165 . If you come from data science background I strongly suggest going through Manolis Kellis (MIT) deep learning for biology course which is public - you will see that a lot of the knowledge you have already is directly transferrable. Having said that, entry is easy (you can follow the advice from the authors book for instance), but to quote Ken, biology gets heavy real fast. What this means there are two learning curves: one relatively small but technical, needed to enter, and one relatively steep, biological, which is needed to be successful. But if you’re interested you won’t mind that as it’s a very fun field.

Wendy Mak

👍 thanks for your perspectives :))

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