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 Update #1: The Math Won (For Now)

The Silence (And The Grind)

djosergenomics.github.io

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-...

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

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

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

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

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.

Field Note 00: Dispatch from the Step Pyramid

Hey everyone 👋 So, something new is happening at Djoser Genomics.

djosergenomics.github.io

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

🥳 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

Djoser Genomics: Year One

Today marks Djoser Genomics’ 1st Birthday.

djosergenomics.github.io

🎉 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

Djoser Genomics@djosergenomics.github.io · last yr.

🧬 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

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 🧪🧫🦠

The Conversation AUNZ@aunz.theconversation.com · last yr.

Over-subscription of a topical antibiotic likely led to the emergence of a superbug which is now the leading cause of resistant infections.

📜 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 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 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 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 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 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 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

Djoser Genomics@djosergenomics.github.io · last yr.

🎊 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

🎊 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

🧬 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

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.

djosergenomics.github.io

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

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 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

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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/

a yellow sign that says we 're hiring

ALT: a yellow sign that says we 're hiring

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🧬💻 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

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,...

embl.wd103.myworkdayjobs.com

🚀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

Discovering Mutations in fisheries-induced Selection of Zebrafish

Zebrafish Variant Calling Training Project

djosergenomics.github.io