NOTE

Dear Users/visitors
Since the fact that at April 2023 Motorola Science Cup has finished (at least for our team), and the project didn't win anything, as well as because of lack of interesst in further development, We've decided to announce its end-of-life. If you're interessted in resuming the development anyhow, feel free to contact us for details.

Thanx!
gucio321 [email protected] - the Head Developer.

Białkomat project is an application written for the Motorola Science Cup competition.

Description

Białkomat is intended to be used for analyzing genetic code typed in or loaded from source file. For more details, take a look at our documentation (required knowledge of polish language).

Unique Selling Point (USP)

1. Handy and self-contained - binary is encapsulated in one executable file that does not depend on your OS*
2. High analysis quality - Our project uses one of the most qualified, open-source Bioinformatics library
3. Innovative technology - the project is a unique combination of 4 programming languages (GO, C, C++ and Python). Such a connection while being a kind of precedent on IT market, still ensures no additional system dependencies needs to be installed.

* Check for System Requirements

Binaries usage

• Go to the latest release and download the file appropiate for your OS.
• extract .zip file using any tool.
• run binary (.exe on Windows and .bin on linux).

System requirements

In order to run one of our binaries, you need to either have access to a 64-bit Windows or Linux Operating System. We also require your OS to support OpenGL and have (at least) 0.5GB free disc space.

Extra flags

You may want to specify some additional flags to see what happens inside of our program.

Usage of ./motorola:
  -help
    	Show this message
  -i string
    	Load data from file
  -info
    	Print app info and exit
  -ll uint
    	Enforce log level
    	0 = Do not enforce (default)
    	1 = Debug (equal to -verbose)
    	2 = Info
    	3 = Warnings only
    	4 = Errors only
    	5 = Practically nothing (prints only fatal errors)

  -no-errors
    	Do not display error messages in app (messages will be logged anyway)
  -skip
    	Automatically skip to Proteins View mode (usually used together with -i)
  -verbose
    	verbose mode
  -version
    	print project's version

So, for example, to load file path/to/data/file.txt and immediately show results in Proteins View (ignoring all the error messages) you can use the following command ./motorla -i /path/to/dat/file.txt -no-errors -skip.

Documentation

Refer to docs.

STATUS

In reference to this document:

• Genetic code reading (35 pts)
• Proteins presentation (25 pts)
• More plots and charts (65 pts)
• Additional things:
  • "Application architecture" (10 pts)
  • documentation (10 pts)
  • UI (25 pts)
  • Unit testing (5 pts)

Compilation instruction

Pre-requirements

for building

• go
• GCC
• mingw (for cross-platform compilation only)
• Python 3.11 (NOTE remember to add it to PATH on Windows)

Source

# download source
git clone [email protected]:TheGreaterHeptavirate/motorola
# change-dir
cd motorola
# download go dependencies
make setup

# run app:
go run github.com/TheGreaterHeptavirate/motorola/cmd/motorola
# OR
cd cmd/motorola
go run .

Python config

You may experience trouble with your binaries, because (for unknown reason) not all operating systems support python3-config command that is used for obtaining right flags. There for please take a quick look at our simple configuration script:

$ go run scripts/flags.go
Usage of /tmp/go-build4250335646/b001/exe/flags:
  -cflags string
    	manually specify CFLAGS
  -ldflags string
    	manually specify LDFLAGS
  -o string
    	output filename (required)
  -pycfg string
    	python3-config executable name/path
exit status 1

-o will be (most often) pkt/python_integration/flags.go And now you need to figure out valid flags. You have three options:

• if your system has pkg-config configured, don't add any flags.
• if you know the exact location/name of python3-config-like script, specify -pycfg
• else you will need to pass the python3-include flags manually with -ldflags and -cflags lets explore this a bit more:
  • C flags specifies where your system should look for Python.h headers. Thats why it should be of the following form: -Ipath/to/python311/includes/, e.g. on Windows 10: -IC:/Users/<your username>/AppData/Local/Programs/Python/Python311/include
  • Linker flags are even more tricky. They should point to python libraries (DLLs on Windows and .so files on linux). Here is a value of -ldflags with that we managed to build Białkomat on Windows 10: -LC:/Users/<your username>/AppData/Local/Programs/Python/Python311/libs -LC:/Users/<your username>/AppData/Local/Programs/Python/Python311 -lpython311 -lm

Alternative - Docker

An official image is available as quay.io/gucio321/bialkomat

As compilation in the way described above may be a bit painful on some operating systems (especially Windows 😄) We've introduced another way to run our application - Docker.

# start immediately
docker-compose up
# you can also construct a large docker command like this:
docker run --name=motorola_app_1 \
--security-opt label:type:container_runtime_t \
--network bridge \
-e DISPLAY=:0 \
-v /tmp/.X11-unix:/tmp/.X11-unix .

NOTE commands above are tested for podman, but since it has the same api as docker, everything should work.

Windows setup

If you wish to run the docker image on Windows, first of all refer to official docker instruction for setting up Docker Desktop on Windows. Then, refer to this page to set up X enviroument and be able to display our app.

important linux note

you need to disable access control for your X envirouemnt, otherwise it will not run:

xhost +