Genomic Prediction for Timothy Grass in Finland

Genomic Prediction for Timothy Grass in Finland

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Timothy (Phleum pratense L.) is a key forage grass for Finnish agriculture, and improving its yield, winter hardiness, and digestibility is crucial for sustainable production. Our recent study explored the potential of genomic prediction to accelerate breeding progress by leveraging genotyping-by-sequencing and advanced statistical models.

Key findings:
* Heritability estimates ranged from 0.13 (yield at first cut) to 0.86 (digestibility at second cut).
* Genetic correlations suggest trade-offs between yield and winter survival but positive links between digestibility traits.
* Genomic breeding values were estimated using advanced statistical approaches, including a novel scaling of the genomic relationship matrix.
* Predictive ability reached up to 0.62 for digestibility, and validation confirmed moderate accuracy with little dispersion.

Despite concerns that genotype quality might impact predictions, our results show that genomic prediction remains a powerful tool for Timothy breeding in Finland. This research highlights the potential for data-driven breeding strategies to enhance forage crop resilience and quality.

https://link.springer.com/article/10.1007/s00122-025-04860-9

New R-package started

New R-package started

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I just started a new R package called ‘SnakebiteTools’. I would like to collect there small helper functions to better analyse and monitor Snakemake runs. The output can later be used for resource optimization, checking the status of an ongoing Snakemake run (which might be messy for runs with plenty of jobs) etc.

Creating Drop-Down Menus in Excel

Creating Drop-Down Menus in Excel

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I often do not remember how to create simple drop down menus in Excel and so I decided to write a short note here. The thing I want to have:

  1. In one tab, I want to have a column with possible values for my drop down menu, e.g my project names
  2. In another tab, I want to have in each button of a column a drop down button that allows me to chose from these values.

This is in principle rather easy to achieve:

Step 1: Prepare the List on Another Sheet

  1. Open your Excel file and go to the sheet where you want to store the drop-down values (e.g., Projects).
  2. Enter the list of values in a column (e.g., A1:A10 in Projects).

Step 2: Name the List (Optional but Recommended)

  1. Select the range of values in Projects (e.g., A1:A10 or the whole column).
  2. Click on the Formula tab → Define Name.
  3. Enter a name (e.g., MyProjects) and click OK.

Step 3: Create the Drop-Down List

  1. Go to the sheet where you want the drop-down (e.g., Tasks).
  2. Select the cell(s) where you want the drop-down.
  3. Click on the Data tab → Data Validation.
  4. In the Allow box, choose List.
  5. In the Source box:
    • If you named the range: enter =MyProjects
    • If not: enter e.g.  =Projects!A1:A10
  6. Click OK.

In case you have in the first line a header (e.g. with column names) you want to remove this line from the drop down options. You can do that like this:

Method 1: Remove Data Validation from One Cell (Header Only)

  1. Click on the first cell of the column (e.g., A1).
  2. Go to the Data tab → Click Data Validation.
  3. In the pop-up, click Clear All → Click OK.
Finding Files in My Folders

Finding Files in My Folders

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Managing disk space efficiently is essential, especially when working on systems with strict file quotas. Recently, I encountered a situation where I had exceeded my file limit and needed a quick way to determine which folders contained the most files. To analyze my storage usage, I used the following command:

for d in .* *; do [ -d "$d" ] && echo "$d: $(find "$d" -type f | wc -l)"; done | sort -nr -k2

Breaking Down the Command

This one-liner efficiently counts files across all directories in the current location, including hidden ones. Here’s how it works:

  • for d in .* * – Loops through all files and directories, including hidden ones.
  • [ -d "$d" ] – Ensures that only directories are processed.
  • find "$d" -type f | wc -l – Counts all files (not directories) inside each folder, including subdirectories.
  • sort -nr -k2 – Sorts the results in descending order based on the number of files.

Why This is Useful

With this command, I quickly identified the directories consuming the most inodes and was able to take action, such as cleaning up unnecessary files. It’s an efficient method for understanding file distribution and managing storage limits effectively.

Alternative Approaches

If you only want to count files directly inside each folder (without subdirectories), you can modify the command like this:

for d in .* *; do [ -d "$d" ] && echo "$d: $(find "$d" -maxdepth 1 -type f | wc -l)"; done | sort -nr -k2

This variation is useful when you need a more localized view of file distribution.

Christmas service in Pälkäne

Christmas service in Pälkäne

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This Christmas we have been to Pälkäne, a little municipality close to Tampere. There is a old church from the 15th century that lost the roof in a storm in the 19th century (as far as I remember from what I read) and now, since 15 years they started using it again for services. However, they plan to build a new (glass-) roof to it, so this year was the last time the service took place in this type.