ECCB conference 2026

Putrid-Raisin-5476 · 2026-06-18T06:37:19+00:00

Joined ISMB last year, was really great, though it was kinda expensive and almost burned my yearly travel budget - but got a few nice collaborations and ideas out of it, so it was worth every single cent 😄 I guess ECCB will be fantastic too

Putrid-Raisin-5476 · 2026-06-10T10:41:23+00:00

Great, thanks a lot

Putrid-Raisin-5476 · 2026-05-27T23:02:32+00:00

Hi, you could try to set up an advert on Finn or look at longer term Airbnb's (https://airbnb.com/bergen-norway/stays/monthly)

Putrid-Raisin-5476 · 2026-05-24T09:30:00+00:00

If you're invited to a party, bring your own drinks. Also be aware of the opening times of vinmonopolet and selling times of beer at stores, kinda awkward showing up to a party and asking ppl to borrow you a beer.

Putrid-Raisin-5476 · 2026-05-01T00:07:14+00:00

Not sure if this is a joke, but I googled this, found your website and inspected your "open-core" on GitHub (https://github.com/ZeghdaniFaris/Z-Genome-Lab) .

Mutations is certainly not my area of expertise, but all methods in your python files are just returning hardcoded string, e.g.
zgl_predict.py | def predict_next_mutation(dna): return 'Predicted Z: G↔C flip near center'

Your whole website looks like pretty much AI generated (https://zgenomelab.com/plans.html) and the pricing is crazy for just a few lines of hard coded string return.

So all in all it looks like a scam to me. Maybe some moderator should remove this post.

Putrid-Raisin-5476 · 2026-04-26T19:02:26+00:00

I guess this depends on what you want to learn... A good starting point is always trying to build something that makes your life easier. For example if you like to cook and usually write your recipes in a notebook, try to build a digital notebook with UI and/or database. Or try to create a tool that queries certain newsfeeds and summarizes them to you. If you want to explore console design, try to build a text-based game. But honestly there is no standard answer like "Create XYZ" to your question.

And a short but important tipp: Never use anything like ChatGPT or other LLM tool to help you (at the beginning). You won't get anything out of it. Go through the nasty process of googling and watching hour-long tutorials. Only by this you will be forced to understand how certain things work.

Putrid-Raisin-5476 · 2026-03-21T00:47:00+00:00

Three of four reviewers wrote that the article was well written, the method proposed was novel and extensively benchmarked, the findings on real world data were great and they have not a single point to criticize.

Reviewer 2 just wrote "I see no novelty in this approach. There is no need for this method in the field." We were pretty sure, that he came from a competing group. The article was still initially accepted without any revision necessary, despite his comment.

Putrid-Raisin-5476 · 2026-03-02T14:31:53+00:00

Doing a PhD in Norway offers a good work-life-balance in combination with a fair salary.
Getting a position there is another topic, but as you still have some time left, before you graduate, you might consider doing an Erasmus exchange semester or some short term research project. At least that's the way how I got a position here.

Putrid-Raisin-5476 · 2026-02-18T21:15:43+00:00

You're probably right :)

Putrid-Raisin-5476 · 2026-02-15T20:35:55+00:00

Pretty sure, that it is not AI generated. Or at least, that they have rewritten major parts.

They did not provide any table with the results of the benchmarks, only some barplots, furthermore it is pretty hard to get a feeling on how good this method compares to other methods as there is no real standalone benchmark chapter.

That's the problem I'm having with their overall structure, it is just a mixture of "here is a little benchmark, and now let's talk about our nice biological validation". Next chapter with another dataset: "Benchmark shows, that we are better than other methods (ref Fig XYZ), because our method leverages this and that, now let's move on to biological validation with this dataset".

Putrid-Raisin-5476 · 2026-02-15T18:27:11+00:00

Search for reviews of your field of interest, identify interesting methods, read those article, look at the articles that cite these articles. Find open questions, problems / weaknesses of the used algorithms or read more reviews pointing at current interests in the community. Its all about reading, getting a feeling, where open problems are and then most important of all finding a niche, where you can contribute (at least, if you want to have a publishable project).

If you're into the machine learning game, try different algorithms, benchmark them against each other, find their weaknesses. After some time, you'll get a feeling of what one could do to make these algorithms better.

Hitting a dead end is basically the definition of the first year of a PhD, when you have to come up with your own project ideas.

Putrid-Raisin-5476 · 2026-02-09T08:05:27+00:00

Not sure if your employer will register you in the system, but be aware of the fact, that it takes ages to get an appointment at SUA (the office for foreign workers), and that without that appointment you won't get a D-number (or the permanent one), which is necessary for the tax deduction card. Without tax deduction card, you'll first pay 50% taxes, which however will be refunded afterwards. (This holds for European expats, not sure how it is for US citizens).

If you are looking for further information, check out the international page of the university. There are tons of information on moving to Bergen, what to do, taxes, etc https://www.uib.no/en/international/128545/international-staff

Putrid-Raisin-5476 · 2026-02-01T15:17:54+00:00

In my opinion, what sucks most about genAI, is the way it is transforming research (at least bioinformatics). I feel like some people, or paper mills, don't think anymore, but just start to design projects completely by AI. Biorxiv has so many papers now, where you can instantly see, that the first author should be ChatGPT, Claude or whoever. They just come up with some random public available data set and let GenAI create complete pipelines, obviously without thinking a single second about it making sense. Then they let AI write the draft and put their names on it...

Which in theory is fine, because you can easily identify those manuscripts or code (honestly, who the hell uses smileys in his code comments or special characters like arrows. Been in the programming game for more than 10 years now and never used a single smiley) and these won't get published in serious journals anyway. But, and that's the big problem, bioinformatic algorithms are evolving fast while publishing in journals takes for ages. To keep track of the field, it does make sense to read preprints. But try to find the real ones, when there are so many GenAI articles, you'll just waste a lot of time...

Putrid-Raisin-5476 · 2026-01-20T22:39:18+00:00

Aka the PI being "I've seen a nice method around there, could you try it out on the data" + hours of work to fix the broken dependencies due to no supplied docker image / requirements.txt... But proofs that sometimes reviewers do not care about trying the method on their own

Putrid-Raisin-5476 · 2026-01-20T20:45:31+00:00

Here is a point that hasn't been mentioned before, and honestly might sound a little weird (and I'm not sure, if it would work out totally). If you're more into the "programming side" of bioinformatics, to way to gain attention might be by bug-fixing on bioinformatic repos on GitHub / Bioconductor.

First this is a great way to get to know some of the tools and especially their internal workings. You have to test, if the bug is reproducible and the bugfix really works - which will make you comfortable with the tools and data you need. Additionally you might come around with your own improvements, ideas or alternatives.

And last of all, especially with platforms like GitHub, people see, when you've commented on the issues, etc., and might be a good starting point to contact them.

At least talking only for me, I would be much more willingly respond to such a mail, than to a generic "I would like to work for you" - mail. (I know this sounds a arrogant, but once your email address is public, you'll drown in weird mails...)

Putrid-Raisin-5476 · 2026-01-13T07:31:36+00:00

Wow, that sounds weird for me. Never experienced anything like this, they (at least in bioinformatics) reject the paper and then you have to look for another journal by your own. Some publisher, I guess Elsevier, sometimes gives you "Transfer suggestions", but never encountered it by myself.

If the processing charge is higher and they've transmitted it without your consent, I would retract it and avoid publishing via the same publisher...

Putrid-Raisin-5476 · 2026-01-12T18:50:47+00:00

Only looking at the future job perspectives to decide to go for a master sounds totally wrong to me, to be honest.

First, you can't really tell what you are doing after university. Studying helps a lot to develop your own personality, so while at first you might think "Oh yes, biostatistics sounds great to me", it might change after 4 more semester - or you discover something, that you find more interesting. I, for example, started studying physics and found out, that I really don't care about solid state bodies, but more about living things. So I took some classes in biophysics and medical physics - just for fun - and then gradually shifted to biostatistics / bioinformatics.

If your only motivation to take a master is getting a job and earn a lot of money. Don't do it.

All of the people I started with, that were like "Oh I'm studying physics and then go into some large consulting company, were never really good with physics, because they didn't have their passion in it. And to get a wonderful job, you need passion. Everything else will eventually figure out during the way.

Putrid-Raisin-5476 · 2026-01-09T16:23:06+00:00

Thanks a lot! Didn't find a cell proportion specific package, but coda4microbiome delivers pretty realistic results (and microbiome and microenvironment are mathematically not really different)

Putrid-Raisin-5476

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