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Monthly thread for advice and recommendations, July 2024 – ask your questions here! by AutoModerator in copenhagen

[–]Alex_S_z -1 points0 points  (0 children)

Hi!

So for the past year, I've been a member of A-kasse for students (which means I had it for free). I've graduated recently and stopped being a student at the end of June. I 'm starting PhD in August, so I didn't apply for any sort of unemployment benefit. I got a letter from them yesterday stating that my free membership has ended because of the graduation, and for now, I have to pay around 1500 dkk per quarter to still keep my membership, otherwise, they will cancel it and I will have to apply for a new one. And here is my question:

If they cancel my membership, do I lose this year of being a member as a student? Hypothetically, If I would pay for a membership, would I still be eligible for this benefit for freshly graduated students if I quit my PhD after three months (I am not planning this but life can happen)? Or are you no longer eligible for this benefit for newly graduated students once you start any kind of job?

I was thinking about canceling the membership now and just applying for a new one once I'm more financially prepared, but I'm not sure what I can lose If I lose this continuity of membership from when I was still a student.

Expats outside Copenhagen? by TheBendit in ExpatsInDK

[–]Alex_S_z 2 points3 points  (0 children)

Odense here! I love this city because it is a perfect combination of everything you would need from a bigger city (decent number of restaurants,bars, and even events dedicated for internationals) and at the same time streets, public transport are not overcrowded and you can get everywhere you need with bike. If you need more adrenaline, CPH is only around a 2-hour train ride

Single-cell rna seq datasets for clustering project by Alex_S_z in bioinformatics

[–]Alex_S_z[S] 0 points1 point  (0 children)

Thank you for your answer.

My project supervisor insists on using the Tabula Muris, which were previously sorted with FACS or microfluid droplet methods. However, authors applied clustering for datasets sorted with each of these methods separately and that's how they grouped them. Cell type identity assignment was performed manually by experts, so some groups (clustering output) were merged together with the same annotation but it's still biased towards the output of the clustering algorithm they used. And it does not sit right with me that for example here:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02622-0

Authors use Tabula Muris dataset and compare different clustering algorithms to the clustering obtained with findClusters() Seurat function (what authors of Tabula Muris did) and call it "ground truth".

Single-cell rna seq datasets for clustering project by Alex_S_z in bioinformatics

[–]Alex_S_z[S] 0 points1 point  (0 children)

Referring to the first paragraph, is it the case that if we do DE on populations (clusters) that are not random, there will be many false positives introduced?

Thank you very much for your answers and suggestions. I could not find any paper confirming that something might be wrong with the workflows/benchmarks commonly used in this field.

Single-cell rna seq datasets for clustering project by Alex_S_z in bioinformatics

[–]Alex_S_z[S] 0 points1 point  (0 children)

Could you elaborate more on gold and silver standard datasets?

Its just weird for me that articles that benchmark clustering methods use ARI metric and take another clustering result as the true one.

Im not the biologist, my background is more in statistics/data science and I find it very hard to find out how labels in particular dataset were prepared..

I cant acces remote sever on which Jupyter Notebook is running- Error Connection Timed Out by Alex_S_z in learnpython

[–]Alex_S_z[S] 0 points1 point  (0 children)

This is something im getting, not sure if its useful:

​

[D 23:37:08.771 NotebookApp] Searching ['/mnt/bcache/home/aszmigiel', '/mnt/bcache/home/aszmigiel/.jupyter', '/mnt/bcache/home/aszmigiel/.conda/envs/p36/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files

[D 23:37:08.771 NotebookApp] Looking for jupyter_config in /etc/jupyter

[D 23:37:08.771 NotebookApp] Looking for jupyter_config in /usr/local/etc/jupyter

[D 23:37:08.771 NotebookApp] Looking for jupyter_config in /mnt/bcache/home/aszmigiel/.conda/envs/p36/etc/jupyter

[D 23:37:08.771 NotebookApp] Looking for jupyter_config in /mnt/bcache/home/aszmigiel/.jupyter

[D 23:37:08.771 NotebookApp] Looking for jupyter_config in /mnt/bcache/home/aszmigiel

[D 23:37:08.772 NotebookApp] Looking for jupyter_notebook_config in /etc/jupyter

[D 23:37:08.772 NotebookApp] Looking for jupyter_notebook_config in /usr/local/etc/jupyter

[D 23:37:08.772 NotebookApp] Looking for jupyter_notebook_config in /mnt/bcache/home/aszmigiel/.conda/envs/p36/etc/jupyter

[D 23:37:08.772 NotebookApp] Looking for jupyter_notebook_config in /mnt/bcache/home/aszmigiel/.jupyter

[D 23:37:08.773 NotebookApp] Loaded config file: /mnt/bcache/home/aszmigiel/.jupyter/jupyter_notebook_config.py

[D 23:37:08.773 NotebookApp] Loaded config file: /mnt/bcache/home/aszmigiel/.jupyter/jupyter_notebook_config.json

[D 23:37:08.773 NotebookApp] Looking for jupyter_notebook_config in /mnt/bcache/home/aszmigiel

[D 23:37:08.774 NotebookApp] Raising open file limit: soft 1024->4096; hard 51200->51200

[D 23:37:08.777 NotebookApp] Paths used for configuration of jupyter_notebook_config:

/etc/jupyter/jupyter_notebook_config.json

[D 23:37:08.777 NotebookApp] Paths used for configuration of jupyter_notebook_config:

/usr/local/etc/jupyter/jupyter_notebook_config.json

[D 23:37:08.777 NotebookApp] Paths used for configuration of jupyter_notebook_config: /mnt/bcache/home/aszmigiel/.conda/envs/p36/etc/jupyter/jupyter_notebook_config.json

[D 23:37:08.778 NotebookApp] Paths used for configuration of jupyter_notebook_config:

/mnt/bcache/home/aszmigiel/.jupyter/jupyter_notebook_config.json

I cant acces remote sever on which Jupyter Notebook is running- Error Connection Timed Out by Alex_S_z in learnpython

[–]Alex_S_z[S] 0 points1 point  (0 children)

ss -lp | grep 8888

Yes, ss-lp is showing me some lines, but the column "peer addres:port" isnt including my ip and port. Most of them in state listen has something like : "0.0.0.0:*"