Software Engineer || Bioinformatics🧬 || Computational Biology🧪.
JavaScript kiddie at NSA ,
Gib me moni
Nov 16, 2024 • 11 tweets • 4 min read
Went home this diwali , decided to convert an old ASUS laptop into a homelab server that I could access remotely.
The idea : host self-hosted apps, VPN, and media servers
First, I made the internal IP static. Went to Ubuntu Wi-Fi settings > IPv4 > Static IP. Set a static addres
Now, the laptop's IP doesn't change after reboots.
Next problem was external IP
Sadly Getting Static ip was too much hassle, so hosting apps with a mapped domain wasn't possible.
DNS providers like DuckDNS are cool, but meh—I wrote my own Dynamic DNS management in node.js
Sep 5, 2023 • 6 tweets • 3 min read
lets deal with this mf now:
so the code has some functions,classes that do some stuff for us caveman's , Awoooga.
also python strong 💪, java weak ☹️
#StereoEnumerationOptions a class->configs how stereoisomers to be generated (you can pass params) 😇 github.com/rdkit/rdkit/bl…
then we have some helper classes, these will be called by others to do :
_BondFlipper-> flips the stereochemistry of a bond
_AtomFlipper -> flips the stereochemistry of an atom.
_StereoGroupFlipper-> flips stereochemistry of a group of atoms associated with a StereoGroup.
Sep 5, 2023 • 5 tweets • 2 min read
the working of the function- `AllChem.EnumerateStereoisomers(input_molecule)`
input -> a SMILES string()
string is first parsed into a RDKit molecule object.
you also use diff params:
-include_cistrans( for geometric isomer)
-include_optical(enantiomers) shorturl.at/qsxG0
internal working for stereoisomers:
- function generates stereoisomers by trying diff combo's( different stereochemical configurations) with rules followed:
1- Chirality : for those with chiral centers, func try's for two possible configurations: R (right-handed) ,S (left-hnd)
Sep 4, 2023 • 5 tweets • 3 min read
yesterday I was able to generate isomer's of some compounds , the input I have 2,3-dichlorobutane in a "SMILE format".
my main focus is on pantoprazole currently.
Those who had GERD or acidic reflux in stomach might have taken this drug.
Its a type of Proton-pump inhibitor.
it binds and forms a covalent bond with something called a proton pump in your stomach and stops the production of H+.
it works like a key and lock thing.
key: pantop and lock : the pump (👉👌)
pretty sure I will fail cause isomers have diff structure and it won't bind same way
Aug 26, 2023 • 4 tweets • 1 min read
wanna know another way to identify viral diseases:
This was used during Covid-19 time , to find what family did Covid came from and if you had it.
remember RT-PCR thing :
getting the initial sequence is the tough, time taking costly part, rest is fast.
India didn't had many labs initially for sequencing , and we struggled for testing .
lol my biotech prof struggled to format the RNA sequence to use it in BLAST.
Python came really handy there.