Project Menhed Update #1: The Math Won (For Now) The Silence (And The Grind)

I haven't posted in a while, and i was in grind against OptKnock so i couldn't do it but i am back! and i have the progress updated!✨

it was mostly about learning, and intro to Metabolic Engineering, and using COBRApy. (and alot of code debugging XD). 🖥️

Check it out! 🚀

Project Menhed Logo

Introducing Project Menhed 🎨

Ancient Egyptian scribes used a palette (Menhed) to mix ink.
I'm using Python to mix genes.

Phase 1: Design a bacteria that produces a Red Dye with high efficiency & 100% In Silico.

I'll share Updates Publicly

Read More 👇

djosergenomics.github.io/Introducing-...

A Darkmode Version of the Djoser Genomics' Logo

Tried out Google's Antigravity today! For a while wanted to introduce a dark mode for the @djosergenomics.github.io Website so decided to let Antigravity's AI Agent take on the task and it performed very well done. Saved me a lot of time indeed!

djosergenomics.github.io

A Schematic Showing a Brief Overview of the Proposed Pipeline

PyMOL Visualization showing the full icosahedral 'shell' of the MS2 bacteriophage (PDB: 2MS2).

PyMOL Visualization showing a single 'monomer' or 'building block' of the MS2 capsid protein. (Yellow is Beta Sheets, Red is Alpha helices, Green is in between loops)

Part of HTGAA Week 4 is to write a proposal on an In-silico Bacteriophage Engineering.

My proposal: 'ArmoredPhage' 🛡️

My goal: Engineer a Thermostable MS2 Bacteriophage Using Protein Design Techniques.

Check it out:
djosergenomics.github.io/Armored-Phag...

#HTGAA #synbio #AlphaFold #proteindesign

PyMOL Visualization of Structures of Tyrosinase Enzyme (Red Alpha Helices, Yellow Beta Sheets, Green In between Loops) (PDB ID: 3NM8)

PyMOL Visualization of Active Sites of Tyrosinase (Copper (II) ions in Orange) - Transparency = 0.35 (PDB ID: 3NM8)

Week 4 of HTGAA (Protein Design) is done & I'm amazed!

I was always intimidated by 3D protein models in papers & never thought I'd understand them one day!

Today, I loaded a PDB file into PyMOL, saw the alpha helices & beta sheets of my Tyrosinase enzyme.

This is so cool. 🚀
#HTGAA #proteindesign

Djoser Genomics Step Pyramid Drawn by Opentrons virtual robot

Week 3 of HTGAA is all about lab automation! 🤖

I wrote a script to program a virtual Opentrons robot to draw my Djoser Genomics pyramid. It simulates robots pipetting 100+ dots of fluorescent E.coli because manually it is slow & error-prone.

#HTGAA #synbio #Opentrons #automation #bioinformatics

I am going to audit the How to Grow Almost Anything (HTGAA) course for my first introduction to my Synthetic Biology journey.

I just did the Bio Bootcamp, & i really loved the interactive sessions on Benchling and Opentrons.

Super Excited for more!
#SyntheticBiology #Bioengineering #MIT #HTGAA

I decided to take a deep dive into Synthetic Biology, Bio & Genetic Engineering, something I've wanted to learn for a while.

I believe it holds incredible potential & innovation for the future if used correctly

Got any tips or resources? :D
#SyntheticBiology #Bioengineering

Field Note 00: Dispatch from the Step Pyramid Hey everyone 👋 So, something new is happening at Djoser Genomics.

Introducing Field Notes from the Step Pyramid!

The target is a space where I can document and share my thoughts, experiences, dreams, & struggles as I navigate through bioinformatics & computational biology.

I will also share snippets from it here to be able to engage with others and learn more.

Been busy with final exams in med school for the last couple of weeks, still not done! But I'll have some time to get back here :)

I've got some new projects and ideas that I'm excited about, so stay tuned! :D

Djoser Genomics: Year One Today marks Djoser Genomics’ 1st Birthday.

🥳 Happy 1st Birthday to Djoser Genomics! 🥳

From starting Djoser Genomics, Learning and Exploring Various Projects, to publishing my first preprint and creating the Bulk RNAseq Tutorial Codex!

Thank you for being part of this journey so far. Here’s to Year Two. 🚀

#Bioinformatics #DjoserGenomics

🎉 The Bulk RNAseq Tutorial Codex is now complete! 🎉

From dataset discovery all the way to enrichment analyses

Every scroll 📜 is now available, covering alignment, quantification, DEGs, visualization & everything in between

The Codex is yours to explore ✨

#RNAseq #Bioinformatics #scicomm

New Zealand’s prescribing habits likely helped create a homegrown #MRSA 🇳🇿🧬💊

Now ‘AK3’ has been detected overseas

Our recent study shows how it evolved & how #Genomics can help reduce the impact of the next ‘superbug’

#AMR is an issue for everyone
#SciComm

🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠

Scroll 8 of Bulk RNAseq Tutorial Codex: Djoser's Discoveries

📜 Scroll VIII: Djoser's Discoveries!

The Grand Finale, we dive into Gene set Enrichment Analysis (GSEA), why we do it, how we do it and how to visualize and interpret it.

Check it out: djosergenomics.github.io/Scroll-8-Djo...

#bioinformatics #RNAseq #scicomm

Scroll 7 of Bulk RNAseq Tutorial Codex: Thutmose's Trends

📜 Scroll VII: Thutmose's Trends!

Here, We identify Trends among our DEGs using Functional (GO) and Pathway (KEGG) Enrichment Analysis!

Check it out: djosergenomics.github.io/Scroll-7-Thu...

#bioinformatics #RNAseq #scicomm

Scroll 6 of Bulk RNAseq Tutorial Codex: Ramses' Plots

📜 Scroll VI: Ramses' Plots!

We dive into Visualizations!

MA, PCA, Volcano Plots and Heatmaps!

Check it out: djosergenomics.github.io/Scroll-6-Ram...

#bioinformatics #RNAseq #scicomm

Scroll 5 of Bulk RNAseq Tutorial Codex: Menkaure's Measures

📜 Scroll V: Menkaure's Measures!

We dive into Differential expression analysis (DEA), using DESeq2, and how to interpret the findings

Check it out: djosergenomics.github.io/Scroll-5-Men...

#bioinformatics #RNAseq #scicomm

Q: What can we learn about plants via metabolomics analysis? 🌱🤔
A: Lots of interesting and useful things! Read our blog to find out what they are:
www.fiosgenomics.com/plant-metabo...

#metabolomics #plantmetabolomics #metabolomicsanalysis #bioinformatics

Scroll 4 of Bulk RNAseq Tutorial Codex: Khafre’s Connections

📜 Scroll IV: Khafre’s Connections is here!

We step into the next stage of our RNAseq journey!
Importing Kallisto results into R, linking them to gene annotations, & building a strong foundation for downstream analysis

Here: djosergenomics.github.io/Scroll-4-Kha...

#bioinformatics #RNAseq #scicomm

Scroll 3 of the Bulk RNA-seq Tutorial Codex: Khufu's Calculations

🧬 Scroll 3 of the Bulk RNA-seq Tutorial Codex is here!

⚒️ Guided by King Khufu, we pseudoalign our reads using Kallisto — fast, efficient, and accurate.

🌐 Full tutorial + cultural spotlight:

📜 djosergenomics.github.io/Scroll-3-Khu...

#RNAseq #bioinformatics #scicomm

Scroll 2 of Djoser’s Bulk RNAseq Tutorial Codex: Hesy-Ra's Diagnostics

🔍 Scroll 2 of Djoser’s Bulk RNAseq Tutorial Codex is here!

We dive into RNA-seq Quality Control with FASTQC — guided by Hesy-Ra, the first known dentist & physician in history.

🧪 Read here: djosergenomics.github.io/Scroll-2-Hes...

#bioinformatics #RNAseq #scicomm

Did you know? 🧠

The Original Step Pyramid that inspired our logo was designed by Imhotep — the same ancient figure featured in Scroll 1 of our Bulk RNAseq Tutorial Codex.

Dive in Now ↓

#RNAseq #Bioinformatics #SciComm

Scroll 1 of Djoser’s Bulk RNAseq Tutorial Codex: Imhotep's Insights

🎊 Scroll 1 of Djoser’s Bulk RNAseq Tutorial Codex: Imhotep's Insights 🎊

We start by collecting real RNA-seq data from ENA using Google Colab.

Inspired by Imhotep - ancient Egypt’s architect of the Pyramid of Djoser.

📜 Check it out: djosergenomics.github.io/Scroll-1-Imh...

#bioinformatics #RNAseq

Djoser’s Bulk RNAseq Tutorial Codex A beginner friendly bulk RNAseq tutorial series told through step by step guides and inspired by ancient Egyptian History.

🧬 Introducing the Bulk RNA-seq Tutorial Codex.

A step-by-step series where I guide you through real transcriptomics analysis, one scroll at a time.

Check out the blog post and follow the codex 👉 djosergenomics.github.io/Bulk-RNAseq-...

#Bioinformatics #RNAseq #scicomm

I'm planning on making a series of mini blog tutorials on bulk RNAseq, they'll be beginner friendly to help someone who's just starting.

I'm also planning to theme it around ancient Egypt just like Djoser ;D

So stay tuned!

#Bioinfomatics #RNAseq

a cartoon character is surrounded by cats and the caption says when someone asks you what your dream job is ALT: a cartoon character is surrounded by cats and the caption says when someone asks you what your dream job is

Only a few days left to apply to join our lab and do exciting senescence research at the University of Cambridge Cancer Research UK Cambridge Institute @cruk-ci.bsky.social @cam.ac.uk 🧪🧬

You can also send informal enquiries (info below):

www.jobs.cam.ac.uk/job/52026/
www.jobs.cam.ac.uk/job/52027/

a yellow sign that says we 're hiring ALT: a yellow sign that says we 're hiring

Spread the news! We are excited to expand our research team, working on cellular senescence, at the Cancer Research UK Cambridge Institute, University of Cambridge.

jobs.cam.ac.uk/job/52026/
jobs.cam.ac.uk/job/52027/

Software Developer In this role, you will have the opportunity to develop domain area expertise in human genetics while working with a modern technology stack. You will design, develop and support the DECIPHER platform,...

🧬💻 We're hiring a #Software #Developer @emblebi.bsky.social! Join the @deciphergenomics.bsky.social team building tools for global rare disease diagnosis & research. Work that matters, in a collaborative environment.
👉 Apply: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
⏰ Deadline: 10 August

Discovering Mutations in fisheries-induced Selection of Zebrafish Zebrafish Variant Calling Training Project

🚀New Blog Post!

Just finished a training project on variant calling using zebrafish data from @uofglasgow.bsky.social study on fisheries selection (PRJNA630223)

Walked through the full pipeline: QC → alignment → variant calling → VEP annotation

#Genomics #Zebrafish #Bioinformatics #VariantCalling