Samuel Nestor Meckoni boosted:
2026-02-12

Celebrate the brilliance of women driving plant sciences forward at Pucker Lab on International Day of Women and Girls in Science! 🌱🔬 Here's to curiosity, innovation, and shattering glass ceilings in STEM! 💪♀️ #WomenInScience #PuckerLab #PlantGenomics #GirlsInSTEM

PuckerLab
Samuel Nestor Meckoni boosted:
de.NBI & ELIXIR GermanydeNBI@mstdn.science
2026-02-10

SimpleVM: Cloud computing without configuration complexity. Set up virtual machines in just a few clicks, run RStudio directly in your browser, manage computational workflows with built-in SNORT-based security. Focus on your research, not infrastructure management. Part of de.NBI's curated bioinformatics services. Learn more: simplevm.github.io/

Samuel Nestor Meckoni boosted:
Boas Puckerboas_pucker
2026-02-09

Need a genome sequence of your favourite plant? We laid out instructions for a complete workflow based on ONT sequencing:

"Cookbook for plant genome sequences"
doi.org/10.1186/s12864-026-126


@PuckerLab
@samnm

Plant genome sequencing workflow. Details: https://doi.org/10.1186/s12864-026-12623-z
Samuel Nestor Meckonisamnm@mstdn.science
2026-02-06

@zerodivision this sounds like you want to do a functional annotation with a reference? Have your heard of the tool GeMoMa? Maybe this might help you, but it needs GFF/GTF files.

Samuel Nestor Meckonisamnm@mstdn.science
2026-02-06

@lwpembleton and with your current job?
I fear that the same fate awaits me when I finish my studies. Luckily my Professor is a Linux advocate :D

Samuel Nestor Meckoni boosted:
Boas Puckerboas_pucker
2026-02-06

Final day of our Python course: Students are presenting individual projects in which they developed tools for the analysis of biological datasets.

The combination of human creativity and thoughtful use of AI led to impressive solutions.

All teaching materials are openly available:
github.com/bpucker/teaching/tr


@PuckerLab
@samnm

Figure summarizing the content of this Python course (AI generated). Teaching materials and additional details are openly available: https://github.com/bpucker/teaching/tree/master/WBIO-A-07.
Samuel Nestor Meckonisamnm@mstdn.science
2026-02-06

@lwpembleton wait a moment... You are using windows? 😅

Samuel Nestor Meckoni boosted:
Mehrad :kde: :emacs: :rstats:Mehrad@fosstodon.org
2026-02-03

There are few practices that deeply hurt me as a Bioinformatician. On top of the list is getting gene expression data in Excel file and figures in PowerPoint file.

I don't know what can it be done and how can it be communicated that not only this is not "okay", but it is a terrible practice because the modifications Microsoft Office Suite does. The situation is so bad that 27 gene names had to be changed because some people are not stopping!

theverge.com/2020/8/6/21355674

#Bioinformatics #Academia

Samuel Nestor Meckonisamnm@mstdn.science
2026-01-28
Samuel Nestor Meckoni boosted:
2026-01-18

Looking for data from @PuckerLab ?

We share genome sequences, annotations, expression data, & other large files via bonndata 📦

🔗 izmb.uni-bonn.de/en/pbb/resear

Open 📊 | Reusable 📁 | Ready for research 🧬

#OpenData #Genomics #Bioinformatics
@researchdata_openaccess
@boas_pucker
@samnm

Digitalis purpurea genome sequence data publication in bonndata. Details: https://doi.org/10.60507/FK2/4KUKXI
Samuel Nestor Meckoni boosted:
de.NBI & ELIXIR GermanydeNBI@mstdn.science
2026-01-16

🚀 Bielefeld University is hiring!
The Genomic Informatics Working Group is looking for a Research Assistant – System Developer (m/f/d). Join a dynamic team at the intersection of genomics & informatics!
👉 More info & application: denbi.de/de-nbi-jobs-portal/20
#JobAlert #Bioinformatics #AcademicJobs

Samuel Nestor Meckoni boosted:
Boas Puckerboas_pucker
2026-01-16

Just 4 days of Python and our students are extracting insights from plant genomics data — all without AI! 🌱

Learn Python & bioinformatics in Bonn:
izmb.uni-bonn.de/en/pbb/contact


@PuckerLab
@samnm

Screens showing the exercises for file handling with Python.
Samuel Nestor Meckoni boosted:
Boas Puckerboas_pucker
2026-01-10

New year, new courses. Getting ready to teach to undergrads again - this time at .

Slides: github.com/bpucker/teaching
More courses: izmb.uni-bonn.de/en/pbb/teachi


@PuckerLab
@samnm

Python course slides. Details: https://github.com/bpucker/teaching
Samuel Nestor Meckoni boosted:
Björn Brembsbrembs
2026-01-07

Für alle, die es vor den Feiertagen verpasst haben:

"Journale wie aus dem Jahr 1665, Preise wie bei MrBeast-Meet&Greets, Datenschutz wie bei Facebook, Verlässlichkeit wie bei TikTok-Lifehacks: Warum es höchste Zeit war, dass die EU die Wissenschaft befreit. Wenn man sie denn lässt."

verfassungsblog.de/rechnungsho

Samuel Nestor Meckoni boosted:
Egon Willighagenegonw@social.edu.nl
2026-01-05

new blog post: "PlantMetWiki: a linked open data service for querying and analyzing plant pathway knowledge" chem-bla-ics.linkedchemistry.i doi.org/10.59350/wyz5v-vts33

"I am happy that Elena and Denise pulled me into a collaboration to create an RDF-based knowledge graph about plant pathways."

tl;dr: plantmetwiki.bioinformatics.nl/

Replying to this post makes it show up in my blog.

#plants #bioinformatics #openscience

Screenshot of the user interface of the linked SPARQL endpoint, showing the logo and name of the project, a large text box to enter SPARQL queries, various colored buttons (to run the query, download the results, etc) and example SPARQL queries on the right-hand side of the page.
Samuel Nestor Meckoni boosted:
2026-01-04

🎉 Happy New Year 2026! 🎉

We are starting the year with great news: several new publications went live over the holidays. A big thank-you to everyone involved in this work!

🔬📄 Explore the latest updates here:
izmb.uni-bonn.de/en/pbb/public

Looking forward to more science, ideas, and exchange in 2026.
@boas_pucker
@samnm

PuckerLab social media banner in Happy New Year 2026 flavor. Many thanks to Marie for the excellent design. Details: https://www.izmb.uni-bonn.de/en/pbb/news
Samuel Nestor Meckoni boosted:
Orhun Parmaksız 👾orhun@fosstodon.org
2026-01-03

Working with biological sequences… in the terminal 🔥

🧪 **SeqTUI** — A terminal-based sequence data viewer & toolkit.

🧬 View, translate, convert to FASTA, extract SNPs & combine huge alignments.

🦀 Written in Rust & built with @ratatui_rs

⭐ GitHub: github.com/ranwez-search/SeqTUI

#rustlang #ratatui #tui #bioinformatics #terminal #cli #opensource

Samuel Nestor Meckonisamnm@mstdn.science
2025-12-31

Happy new year! Just repotted my Nicotiana benthamiana plants that I will use for #research next year! They are my most favorite root-harboring model organism 😁
What is your most favorite model organism?
#nicotiana #plantscience #modelorganism

Two small pots with each 10 small green plants in them. The black earth contains white crumbles. Some blurry labeling is at the top of the picture and the pots are labeled with an ID.Many small pots each with one tiny green plant. The black earth contains white crumbles. The first pots have labels with an ID.
Samuel Nestor Meckoni boosted:
2025-12-20

Our digital Christmas tree this year is built from squares inspired by performance indicators in our ONT sequencing experiments 🎄📊
In 2025, sequencing output increased substantially — a great way to close the year!

More on the design idea and other news:
izmb.uni-bonn.de/en/pbb/news#t

#OpenScience #Sequencing #DataArt #Christmas #LabLife
@boas_pucker
@samnm

Our Christmas tree is this year inspired by squares indicating the performance in our ONT sequencing experiments. Details: https://www.izmb.uni-bonn.de/en/pbb/news#tree2025
Samuel Nestor Meckoni boosted:
Boas Puckerboas_pucker
2025-12-12

Our course “From Gene Models to Biological Insights – Functional Annotation” has officially concluded! Proud to have supported 20+ early-career researchers in developing their skills in plant genomics. 🌱🧬
Looking forward to seeing their discoveries!

izmb.uni-bonn.de/en/pbb/news#d

@PuckerLab
@samnm

Impressions from our "From Gene Models to Biological Insights - Functional Annotation" course. More details: https://www.izmb.uni-bonn.de/en/pbb/news#d2025c2

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