Dominik Buchner
@dominikbuchner.bsky.social
Staff reasearcher at @leeselab.bsky.social
studying molecular biology, bioinformatics, and robotics. Developing tools to democratize molecular biology.
studying molecular biology, bioinformatics, and robotics. Developing tools to democratize molecular biology.
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.
January 29, 2025 at 1:38 PM
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.
It's working 😍
January 29, 2025 at 1:37 PM
It's working 😍
January 29, 2025 at 1:37 PM
While producing similar results we were able to boost performance almost tenfold compared to other well known pipelines. APSCALE scales well with dataset size in terms of runtimes and ressources needed. Make sure to check out the benchmark!
January 29, 2025 at 1:37 PM
While producing similar results we were able to boost performance almost tenfold compared to other well known pipelines. APSCALE scales well with dataset size in terms of runtimes and ressources needed. Make sure to check out the benchmark!
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
January 29, 2025 at 1:37 PM
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
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
January 29, 2025 at 1:37 PM
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
January 29, 2025 at 1:36 PM
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
Finally, we have not one but four!!! 96-well gel chambers 😍🧑🔬@leeselab #upscaling
January 29, 2025 at 1:36 PM
Finally, we have not one but four!!! 96-well gel chambers 😍🧑🔬@leeselab #upscaling
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/
mbmg.pensoft.net/article/67533/
January 29, 2025 at 1:36 PM
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/
mbmg.pensoft.net/article/67533/
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🙃!
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🙃!
January 29, 2025 at 1:36 PM
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🙃!
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🙃!
Results also look nice 🙃🙃
January 29, 2025 at 1:36 PM
Results also look nice 🙃🙃
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 🦾🧑🔬🧬
January 29, 2025 at 1:36 PM
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 🦾🧑🔬🧬
New lighting for our #biomek @leeselab. Will be even more fun to program this machine now ☺️🖥️🕹️⌨️ #upscaling #hightroughput
January 29, 2025 at 1:35 PM
New lighting for our #biomek @leeselab. Will be even more fun to program this machine now ☺️🖥️🕹️⌨️ #upscaling #hightroughput
Take that, soil! #TNA #soilsamples #beadbeating #finally
A lot of bead-beating does the trick @teamBOMBbio
A lot of bead-beating does the trick @teamBOMBbio
January 29, 2025 at 1:35 PM
Take that, soil! #TNA #soilsamples #beadbeating #finally
A lot of bead-beating does the trick @teamBOMBbio
A lot of bead-beating does the trick @teamBOMBbio
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.
January 29, 2025 at 1:35 PM
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.
DIY size selection @leeselab. Things really starting to work out with our DIY-Beads @teamBOMBbio.
January 29, 2025 at 1:35 PM
DIY size selection @leeselab. Things really starting to work out with our DIY-Beads @teamBOMBbio.
Same protocol, DNA extraction from tissue. One dropout, some adjustments needed but in theory enough beads for 50.000 extractions for ~ 200€. With implementation on our #biomek @leeselab 96 extractions in less than 30 minute😊
January 29, 2025 at 1:35 PM
Same protocol, DNA extraction from tissue. One dropout, some adjustments needed but in theory enough beads for 50.000 extractions for ~ 200€. With implementation on our #biomek @leeselab 96 extractions in less than 30 minute😊
Cryogenic bead-beating #eDNA filters and extracting from the dust look very promising. Way faster and less prone to cross-contamination! @leeselab
January 29, 2025 at 1:35 PM
Cryogenic bead-beating #eDNA filters and extracting from the dust look very promising. Way faster and less prone to cross-contamination! @leeselab