First sour-dough bread

First sour-dough bread

I am currently trying out, how to create a sour-dough bread from scratch. For that, I first started my sourdough starter by mixing 50g rye flour and 50g water into a bowl with loose lid and kept it in our warm, technical room. After 24h I added again 50g rye flour and 50g water, mixed it and put it back to the technical room for 24h. Then on the second day, I added 100g of rye flour and 100g of water (just to remain the 1:1:1 ratio, indicating that the existing sourdough should match the newly added flour and water). On the third day, I took then 200g of the mixture away and added again fresh 100g flour and 100g water. That I did in total three times. During the time I could see that the dough started to small sourish, beer-alike with the fruity note, so not bad at all. When that happened, I decided to go for the first bread.

I mixed in the lunch break

  • 100g sour-dough
  • 300g Wheat flour
  • 200g Rye flour
  • 350 ml water
  • 12g salt

and placed it for resting 30 minutes (covered with a towel in a bowl). Then I roughly folded and pulled it and placed the dough a cast-iron pot with a floured bottom. That bowl I covered again with a towel and let it rest at room temperature until evening (for about 6 hours). Then I placed the dough in the casst-iron pot into the fridge to let it rest for the night.

On the next day in the morning, I took out the pot to let it warm up a little at room temperature (for about an hour, during breakfast). Here I also sprinkled some wheat flour over it and cut some stripes into it. I then pre-heated the oven to 230 degrees and placed water in the bottom of the oven (I have an oven that has a build-in water bowl to steam, it is a bread program). Once it reached temperature, I added the pot (without lid) into it and backed the bread for about 20 minutes. Then I lowered the temperature to 200 degrees and backed for another 25 minutes.

From the remaining started, I took another 100g away, leaving me with 100g remaining starter, where I added again 100g flour and 200g water, placed it in a warm room for 3-4 hours and placed it then into the fridge.

When I bake then next week, my plan is to out 50g one day before baking day, add 50g flour and 50g water and let it activate 24h. From there I can take then 100g for the backing again. The root I’ll keep then in the fridge, but here I need to see still how to keep it fresh and happy in the fridge.

eggNOG7 annotator script

eggNOG7 annotator script

For our metagenomics pipeline I wrote a quick and dirty annotator script that can be found here and which might be useful for one or another.

https://github.com/fischuu/eggnog7_annotator

The purpose of the tool is that it takes protein sequences from gene predictions and annotates (in the sense of intersects) them with known proteins, their functions and taxonomic origin. That way, the tool can be used to shed a bit of light on plain protein sequences.

The current eggNOG annotator uses only the database version 5 and was not available for version 6. Now eggNOG 7 was pulbished and we thought within out MetaG pipeline group that it would be good to have a db7 annotator, so we added it to the pipeline and have from that also this stand-alone version linked here.

Understanding Whitefish in the Northern Baltic Sea

Understanding Whitefish in the Northern Baltic Sea

A new article I contributed to has been published in Fishery Research.

The study focuses on European whitefish in the northern Baltic Sea, which exist as two types, or ecotypes: one that migrates between rivers and the sea (anadromous) and one that spawns entirely in the sea. These fish are caught together in fisheries, but the river-migrating type is endangered, while the sea-spawning type is doing better.

We looked at ways to tell the two types apart, using both physical traits and genetic data. This isn’t always straightforward — some fish show mixed traits, likely due to past stocking, habitat changes, or variable migration patterns. We also studied how fishing depth, season, and net size affect which type of fish is caught. The results show that fishing practices can strongly influence catch composition, highlighting that adjusting fishing rules by location and timing could help protect the vulnerable whitefish population.

The full article is available on ScienceDirect:
https://www.sciencedirect.com/science/article/pii/S0165783626000019