iiinova — where your digital self keeps evolving

Reposted by Dominik Buchner

Rudolf Meier @rudolf-meier.bsky.social · 14/03/2025

🚨 EntoSieve is now published in Molecular Ecology Resources: Fast and accurate size-sorting of bulk insect samples! Perfect for boosting DNA megabarcoding & metabarcoding projects. 🧬🔬 DIY low-cost device, gentle on specimens and yet efficient 🦋🐞 here: onlinelibrary.wiley.com/doi/full/10....

2349

Dominik Buchner @dominikbuchner.bsky.social · 24/02/2025

I just released version 3.0.0 of the upscale pipeline. It now implements optional replicate merging and the automatic removal of reads found in the negative controls. Check the details on my GitHub. github.com/DominikBuchn...

github.com

Release 3.0.0 released · DominikBuchner/apscale

apscale can now automatically merge replicates and remove the maximum number of reads found in the negative controls the respective tab in the settings file has been added: 7_replicate_negative_con...

050

Reposted by Dominik Buchner

Florian Leese @leeselab.bsky.social · 21/02/2025

Tolle #Biospektrum Ausgabe zu Hochduchsatzsequenzierung mit Review von @dominikbuchner.bsky.social & mir zu #Biodiversität #Monitoring mit #Metabarcoding Wir betonen 3 besonders wichtige (& einfache) Schritte zur Qualitätssicherung & 4 nächste Schritte (nicht alle einfach). tinyurl.com/ht-biodiv

041

Dominik Buchner @dominikbuchner.bsky.social · 06/01/2023

Just released version 1.6.0 of the APSCALE pipeline. This update includes improved log writing and added failsafe features for better handling of invalid settings. Check it out on GitHub:#apscale #metabarcoding #pipeline github.com/DominikBuchner…

github.com

GitHub - DominikBuchner/apscale: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - DominikBuchner/apscale

043

Dominik Buchner @dominikbuchner.bsky.social · 05/01/2023

We're happy to share our RNA cleanup protocol on @protocolsIO! Our method is significantly more cost-effective than commercial kits, without sacrificing effectiveness. Check it out here:#RNA #cleanup #openscience @leeselab protocols.io/view/rna-clean…

protocols.io

RNA cleanup with magnetic beads

This protocol describes cleaning up RNA extracts with carboxylated magnetic beads and a PEG-NaCl buffer. It can also be used for volume reduction of a sample or buffer exchange...

000

Dominik Buchner @dominikbuchner.bsky.social · 30/11/2022

Twitter, your help is needed: I'm desperately searching for small-volume, gravity-flow anion exchange columns comparable to the JetStar columns in the Qiagen RNeasy PowerSoil Total RNA Kit. Does anyone know a supplier for those columns?

000

Dominik Buchner @dominikbuchner.bsky.social · 18/11/2022

Co-extracting DNA/RNA from sediment haunted me for almost 2 years now with limited success so far. This changed today: I finally developed a protocol to process up to 15g of sediment in one extraction while splitting up DNA/RNA along the way. Will sleep like a baby tonight.

200

Dominik Buchner @dominikbuchner.bsky.social · 24/10/2022

Sales representative:"How many plates do you need?" Me:"Yes" #upscaling

000

Dominik Buchner @dominikbuchner.bsky.social · 13/10/2022

Since everyone is talking about open science these days and I fully agree that knowledge should be accessible to anyone I will start putting all protocols I know on @protocolsIO. DNA extraction and bead cleanup are already up. Will add more gradually. 👨‍🔬🙂 protocols.io/researchers/m4…

protocols.io

Dominik Buchner on protocols.io

Metabarcoding, Genetics, Bioinformatics, Robotics

000

Dominik Buchner @dominikbuchner.bsky.social · 16/09/2022

Update on #BOLDigger: For the selection of any type of top hit all database entries containing punctuation and/or numbers will be ignored. This leads to cleaner taxa lists and less data cleaning needed for final analysis 🤓

000

Dominik Buchner @dominikbuchner.bsky.social · 29/08/2022

APSCALE is now published in Bioinformatics. Feel free to try out our metabarcoding pipeline, give feedback or tell us what to improve. Finally published sth in 2022 🥳💻@leeselab @TillMacherr academic.oup.com/bioinformatics…

academic.oup.com

APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data

AbstractSummary. DNA metabarcoding is an emerging approach to assess and monitor biodiversity worldwide and consequently the number and size of data sets i

102

Dominik Buchner @dominikbuchner.bsky.social · 07/08/2022

When the mainboard of your (real) computer is determined to commit suicide, so you are forced to spend the last weekend of your vacation backing up data and disassembling it. Good excuse to buy a new computer though 🥲🥲 #goodbyeoldfriend

000

Dominik Buchner @dominikbuchner.bsky.social · 24/05/2022

Updated BOLDigger and BOLDigger command-line to version 2.0.0. Selection of the top hit is now more sophisticated, check out the Readme for a detailed description of the function. Command-line version is now as quick and functional as the GUI. #BOLDigger #python #metabarcoding

000

Dominik Buchner @dominikbuchner.bsky.social · 16/05/2022

Started to work on automatic image annotation as a side project. Got serious quickly. Ordered an LED table and took photos with my cell phone. Works pretty well already, still need to add a scale to measure insects in mm instead of pixels 🤓#python #opencv #malaise @leeselab

000

Dominik Buchner @dominikbuchner.bsky.social · 09/05/2022

Time to learn some new (and hopefully exciting) stuff. I promise to stop using this as soon as I have my PhD. Good to know that this will still take a while 😁 #coding #ai #python

000

Dominik Buchner @dominikbuchner.bsky.social · 14/02/2022

#BOLDigger update: Asynchronous requests are now implemented into #BOLDigger speeding up the identification engine 2-4 fold, depending on internet connection and database availability. Up to 1000 sequences per hour are now possible! @leeselab

100

Dominik Buchner @dominikbuchner.bsky.social · 18/01/2022

Check out our metabarcoding pipeline #apscale. Finally found the time to close the gap between my demultiplexing tool and #BOLDigger. Easy to install, option to run an all-in-one analysis from demultiplexed read to the OTU/ESV table. @leeselab github.com/DominikBuchner…

github.com

GitHub - DominikBuchner/apscale: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - DominikBuchner/apscale

100

Dominik Buchner @dominikbuchner.bsky.social · 24/12/2021

All I want for Christmas is ~ 500 GB of raw read data or ~ 3.5 billion PE reads to demultiplex. #merrychristmas @leeselab #malaisetraps #bigdata

000

Dominik Buchner @dominikbuchner.bsky.social · 03/11/2021

It took me 9 full working days to extract 3316 Malaise Trap samples. Lessons learned: Sleep is not that important. Maybe it's time to scale down. I need to lose some (more) weight. 36 plates of PCR incoming. @leeselab #upscaling #insectmonitoring #metabarcoding

000

Dominik Buchner @dominikbuchner.bsky.social · 22/09/2021

In our new study, we show how to automatize metabarcoding pipelines on liquid handlers. We used two datasets to demonstrate the high reproducibility and robustness of our workflow. Great to finally see this paper published! 🙃🧑‍🔬🧬🕹️@leeselab @TillMacher sciencedirect.com/science/articl…

000

Dominik Buchner @dominikbuchner.bsky.social · 20/08/2021

Finally, we have not one but four!!! 96-well gel chambers 😍🧑‍🔬@leeselab #upscaling

000

Dominik Buchner @dominikbuchner.bsky.social · 20/07/2021

Looking for a cheap and efficient way to homogenize invertebrate bulk samples?! We developed a cheap and time-saving homogenization and cleaning protocol using a common kitchen blender. 🧑‍🔬🧬 #upscaling #metabarcoding @pipette_jockey @leeselab mbmg.pensoft.net/article/67533/

100

Dominik Buchner @dominikbuchner.bsky.social · 04/04/2021

Update on #BOLDigger: Took the easter break to fix the most common issue amongst #BOLDigger users: Invalid sequence names or invalid characters in sequences. #BOLDigger will find these now and correct them if needed. Input on new features always welcome🙃!

000

Dominik Buchner @dominikbuchner.bsky.social · 24/03/2021

TNA extraction on our #biomek @leeselab. No space left on the deck, even had to start with stacked plates. Input: 96 GITC lysed samples | Output: RNA plate, DNA plate, quality control plate. 96 samples take 3h. Good way to start the week 🦾🧑‍🔬🧬

100

Dominik Buchner @dominikbuchner.bsky.social · 07/03/2021

The only advantage of websites not providing a working #API is that I can improve my programming skills #python #givemethatdata

000

Dominik Buchner @dominikbuchner.bsky.social · 26/02/2021

New lighting for our #biomek @leeselab. Will be even more fun to program this machine now ☺️🖥️🕹️⌨️ #upscaling #hightroughput

000

Dominik Buchner @dominikbuchner.bsky.social · 22/01/2021

TNA extraction with BOMB beads @teamBOMBbio. No success with soil samples yet but perfect TNA from caddisflies. Takes 1.5 h to complete, possible in under an our if done on our #biomek.

000

Dominik Buchner @dominikbuchner.bsky.social · 21/12/2020

DIY size selection @leeselab. Things really starting to work out with our DIY-Beads @teamBOMBbio.

000

Dominik Buchner @dominikbuchner.bsky.social · 09/12/2020

Looks legit 😎 @leeselab . Some adjustments for size exclusion needed but at least the beads seem to bind DNA. Buffers were taken from a spin-column kit. Looking forward to testing our costum protocols 🧐🧐 @teamBOMBbio #DIY #cooking

100

Dominik Buchner @dominikbuchner.bsky.social · 08/12/2020

Trying to synthesize our own magnetic beads with silica-coating @leeselab . Hopefully will be successful @teamBOMBbio #DIY

000

Dominik Buchner @dominikbuchner.bsky.social · 14/10/2020

Cryogenic bead-beating #eDNA filters and extracting from the dust look very promising. Way faster and less prone to cross-contamination! @leeselab

120

Dominik Buchner @dominikbuchner.bsky.social · 02/10/2020

Ran thousands of qPCR reactions in the last few days @leeselab. Thanks for editing the video @THM_93. #robotics #biomek #qpcr Pipetting a qPCR on a Biomek FXP Liquid Handling Workstationvia @YouTube youtu.be/xO2ylnmADos

youtu.be

Pipetting a qPCR on a Biomek FXP Liquid Handling Workstation

Absolute quantification of template copy numbers utilizing the Biomek FXP

000