Implementing a High Performance Sequence Aligner in C++
Building a High-Performance Sequence Aligner
Oromidayo Owolabi
Programmer
Latest posts
Optimizing my Database Engine Pt 1
A while back, I wrote a toy polymorphic database engine in Rust. It’s purpose was to enable CRUD operations on document and relational row and columnar formats, in one DB. I wrote the paging system, interpreter, query executor, and client. But it wasn’t very efficient. I can’t remember just how bad it was but going by the popular saying “If you can optimize something 1.5x, thats good. If you can…
Understanding Attack Surfaces
Before taking the OMSCS cybersecurity course, I thought I had a reasonable understanding of security. We used HTTPS, sanitized inputs, signed JWTs, rotated secrets, ran vulnerability scans. Security felt like something you layered onto a system once the “real” engineering was done.
High Performance Bioinformatics (4) - Parallel Computing
Parallel computing is essential in high-performance bioinformatics, enabling faster processing of large datasets. If you’re looking for a deeper dive into parallel computing and heterogenous platforms, I recommend this book:
Think API First
In my past couple of months programming web backends and systems projects, working a bit on open source, and reading larger codebases, I have reshaped my premature thinking about coding and programming in general.
Writing a Polymorphic Database Engine in Rust
So, I did a batch at the Recurse Center earlier this year. My main goal going into the batch was to work on some performance-based software engineering, and to learn more about low-level systems stuff. Knowing no Rust, and wanting to deepen my knowledge in database systems, I spontaneously arrived on this as a project at day one.
Why Does fib(40) Elude My Sh*tty Interpreter
> TL;DR: C++ performance is hairy for tons of small object allocations / deallocations especially when the compiler cannot intuit what you are trying to do Ahead-of-Time. Memory pools might resolve this issue but for nested calls finding free objects to acquire is tougher. Rust also performs poorly in this scenario. The JVM is king at this kind of problem thanks to the JIT and Garbage Colector.
The Art of Memory Palaces and Mental Visualization
I have been using memory palaces extensively for over 3-4 years now. I first discovered them while going through the book “Moonwalking with Einstein” by Joshua Foer. Back then I was very interested in finding ways to read and absorb information faster to become a superlearner, enhancing my performance. As a sophomore year engineering student taking courses that required some physical intuition…
2022: A Book Year in Review
According to my Goodreads account, I managed to read about 45 books this year. While maintaining my usual bursts in reading frequency, I still managed to get through some pages. I think what really helped me this time was having a good bunch of books I really wanted to get through, and even though I did not remain faithful to that original list, it gave me the drive to read more.
1984 by George Orwell
1984 is a powerful and thought-provoking novel that explores the dangers of totalitarianism and the effects of government control on the individual. The story follows the struggles of Winston Smith, a man who is aware of the horrors of the dystopian world he lives in. We see him struggle to conceal his unorthodox and unacceptable manners. We see him fall in love with another rebelled. We see him…