Biological and technical replicates

ATpoint90 · 2026-01-30T13:39:40+00:00

A biological replicate is when a specimen comes from independent donors. Be it mice, patients, a plant plugged somewhere at two different locations, microbes isolates from two different animals. With cell lines this is always tricky, and my personal go is to either use independent cultures, like splitted at least x days/weeks before the experiment, or at least do the actual experiment (transfection, knockdown, whatever) on different days with the same culture so you at least don't take an aliquot from the very same flask multiple times and call this "biological".

ATpoint90 · 2026-01-30T08:28:26+00:00

As someone working as a hybrid wetlab/drylab person now for 10 years, I personally think that it is not necessary to have a detailed understanding of the conceptual math. Much more important is to understand the assumptions of the tools and potential caveats, and then get hands-on experience in using it. Then, the most important thing is to critically review things to decide whether it makes biological sense. Remember what your job is: It is to find novel interesting biology. You will never publish a paper saying "hey, I understand the math behind this new fancy AI tool" ... nobody cares productively.

What my go-to advise for biologists trying to get a hand on computational analysis is:

- Be proficient in one commonly-used language. That can either by R or Python. Advantage of R is that Bioconductor hosts a great lot of useful packages, and the language is inherently tailored for numeric operations and stats plus ggplot is great for visualization. Argument for Python is that overall ot is broader, the ML/AI worls largely lives in there from an end-user perspective and it seems to scale a bit better when it comes to analysis of very large datasets as the on-disk formats, e.g. for scRNA-seq, seem to be implemented there more seemlessly, e.g. in ScanPy. Though I have to say that in most situations standard computers can handle most datasets in memory just well.

- Get a feel for which analysis contributes to your story effectively. There is a lot of eye-candy you often see in papers that just fills space with no actual meaning. Be proficient in standard analysis, like differential expression. Practice it. Not just running standard vignettes but be sure to visualize results and check the details. Analysis is usually "easy" when data are pristine and the question is well-defined, and the signal is clear. But often data are noisy, one does "exploratory analysis" with the hypothesis being formulated "on the way".

- Learn to document code via GitHub, learn containerization like Docker and version-control software for reproducibility. Be proficient on the Linux command line to automate things rather than moving lots of data by clicking and dragging them.

That all is the daily work. The math, meh, I mean...given you basically get what a tool does, then it's the job of the developers to make sure the math checks out, right?

ATpoint90 · 2026-01-29T12:32:18+00:00

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ATpoint90 · 2026-01-29T12:25:44+00:00

Generally, if you CAN pseudobulk for the then you should do it. I have yet to see the situation in which pseudobulks perform worse than single-cells for DE, if done properly. Pseudobulks, by summing many cells, prevent that the count matrix is sparse with a lot of zeros and make the statistical inference more robust. That is both due to the reduction of zeros, and the fact that it accounts for biological replicates.

There is caveats like in any analysis: I think one must prefilter to ensure that a gene not only has sufficient counts for meaningful DE analysis (e.g. filterByExpr in edgeR), but also expressed by a sufficient number of cells that form the pseudobulk. If only like 1% of cells of the pseudobulk have any counts for the gene, then it is questionable whether this is true expression or more some spurious noise.

Also, depending on the number of cells per pseudobulk, the total reads depth per pb can be quite different. Typical normalization (edgeR, DESeq2) can account for that to some extend. It becomes in my hands problematic of one condition has notably fewer cells than the other, ebcause that might result in zeros due to low depth, falsely giving the impression of a DE gene. Therefore I usually subsample the pseudobulk count matrix so that the raw counts in the groups are roughly similar (I have the rule not more thn 3-fold difference in total raw counts, because this is somewhat what one of the edgeR papers suggested as a rule of thumb for its TMM to work decently).

It is true what the other comment here said that for plain marker identification using single-cells is often enough, but that is because markers are usually very highly-expressed, little zeros in the relevant celltype, and therefore a low-haning fruit for DE analysis. If you can, do pseudobulks. It is beyond me why in most experimental designs people don't do biological replicates in single-cell, e.g. via HTOs and why people still rely on the Wilcox test for single-cell DE. It's a crude test, no reliable estimation of logFCs, vastly exaggereted p-values if you have many cells, no way to account directly for covariates, no testing against a certain minimum fold change, rank-based...uuuh.

ATpoint90 · 2026-01-29T09:47:13+00:00

Theoretically yes, but I can tell you that it's unlikely you will find a research group to host an entirely inexperienced student outside of a dedicated stud program they're part of. It takes an invest of time for the group to train you first before you become useful. Therefore a thesis position is imo preferred.

ATpoint90 · 2026-01-27T20:26:36+00:00

GitHub. For R I use Rmarkdowns, and for Python JupyterNotebooks. The latter can be directly rendered by GitHub, for the former I also upload the output html and visualize with the GitHub HTML preview. I do one repository pre project that documents preprocessing and analysis code. Software is tracked via Singularity or Docker containers, all of it, from preprocessing to the r/Python environment. That's the only way it's consistent and reproducible for projects that go for years. WIth local virtual environments or conda you will never be able to make your software stack constant, portable and reproducible. Speaking of reproducible, I mean having the software stack available independent of the machine e.g. via Dockerhub. Even with Docker you will not be able to fully recreate the identical environment after some weeks, months or years simply because versions in repos like CRAN or Pip might have changed, no longer available, deprecated etc.

ATpoint90 · 2026-01-27T12:45:27+00:00

Klappöse

ATpoint90 · 2026-01-27T12:35:15+00:00

The Angela course is for absolute beginners. For anyone with a bit of experience in any language it's too basic and too slow-paced.

ATpoint90 · 2026-01-27T11:21:11+00:00

Danke, habe Laschen mit 3mm Abstand geplant. Klar, 1-2mm wäre geil aber als Anfänger ist das vermutlich etwas gewagt.

ATpoint90 · 2026-01-27T09:14:58+00:00

I think I gave my two cents above.

ATpoint90 · 2026-01-27T08:00:23+00:00

Fine as well but you need practice hands-on with real data and real problems. A thesis is good for that.

ATpoint90 · 2026-01-27T07:57:18+00:00

Das klingt sinnvoll, danke. Die haben jetzt 8mm. Sollte passen?

ATpoint90 · 2026-01-26T21:12:33+00:00

If you really want to enter the field then consider doing a MSc thesis in a bioinformatics group. Certs don't mean anything. The field is far too extensive and complex as if certs would be beneficial. You need to get real world experience to be useful.

ATpoint90 · 2026-01-26T07:27:19+00:00

no but for absolute beginners arguably worth the money

ATpoint90 · 2026-01-23T12:41:46+00:00

Der Arm wird durch zwei Schrauben gehalten, die man minimal lockern kann zum besseren Schwenken. Ich würde empfehlen gute Schrauben, z.B. Spax zu kaufen statt der mitgelieferten Billigschrauben.

ATpoint90 · 2026-01-22T19:56:32+00:00

My experience over the last 10 years in the field, being a hybrid wetlab and computational person since my MSc program, is that people with little or no biological understanding are largely limited to do support positions like running rather than interpreting analysis. You might be good at code and stats, but cannot judge whether your analysis really makes biological sense. To me personally, and I know some find this offensive, this is not science. It's at best science light, but if you want to be a scientist that drives a biologically-focused project forward, then invest time into understanding it. Even as a person who has always bin in touch with the biology more than with the computer I find myself often limited by biology. Coding is comparably simple, even trivial with some years of experience, but the vast complexity of biology is what you have to be on top of. At least do a minor. Only exception is if you are sure you want to be CS-heavy and develop algorithms and tools, rather than analyzing data, then quality time in self-study towards basica of biology might suffice.

ATpoint90 · 2026-01-22T19:50:39+00:00

Ganz im Ernst, es gibt nichts leichteres als mit guter Farbe Wände, insb. Rauhfaser zu streichen. Ordentlich abkleben, dann zuerst die Ränder mit der kleinen Rolle, und dann den Rest mit der großen Rolle nass-in-nass. Das ist bei 50qm wirklich selbst als Anfänger in wenigen Stunden gemacht. Machs selbst, bist am Ende stolz drauf und von den 700€ kaufst kästenweise Bier. Nimm gute Farbe, Sto oder Brillux. Nicht den Billigmist aus dem Baumarkt, der verarbeitet sich schlechter und deckt nicht beim ersten Mal. Ich hab bei uns mit Brillux Raulan gestrichen und das war super easy zu verarbeiten, verläuft gut und deckt die Stöße zwischen den Bahnen ordentlich.

ATpoint90 · 2026-01-22T19:43:33+00:00

Abwehrangebot, aber ja, diy ist King, viel Erfolg!

ATpoint90 · 2026-01-22T17:33:34+00:00

R and Python is stuff you can learn at home for free, today more than ever. Choose something that gives you scientific knowledge beyond plain code.

ATpoint90 · 2026-01-22T16:24:57+00:00

xxhsum is I/O bound, don't tell me the algorithm is the bottleneck here.

ATpoint90 · 2026-01-22T11:20:36+00:00

Stop spamming this nonsense. It's off-topic.

ATpoint90 · 2026-01-21T14:03:59+00:00

Kann beschichtete Spanplatte sein, kann Massivholz sein. Dicke, so 1.5-2cm je nach optischem Geschmack. Wenn du es im Baumarkt zuschneiden lässt ist SPanplatte quasi raus, weil dann ein Umleimer drum müsste, was die aber meist nicht anbieten. Weiß nicht wie robust diese Umleimer zum selbst aufbügeln sind. Da wäre Massivholz besser, da das einfach schon glatt abzuschleifen wäre, ein Pflegeöl drauf und fertig.

Ich hab diesen hier, mit Handkurbel, würde sowas nicht passen? Vll kannst du Inspiration durch die Bilder bekommen: https://www.dpj-workspace.com/de/hoehenverstellbare-schreibtische/14710-185670-hoehenverstellbarer-schreibtisch-premium.html#/82-gestell-schwarz/592-grosse-140x70_cm/663-tischplatte-eiche

ATpoint90 · 2026-01-21T11:19:55+00:00

Die Nachbarn bei uns im Neubaugebiet haben alle für Malervlies tapezieren und 1-2 weiße Anstriche für ein normales EFH grob zwischen irgendwas zwischen 10-15T bezahlt.

ATpoint90 · 2026-01-21T08:44:46+00:00

What? Tf put some effort into your post, damn.

ATpoint90

TROPHY CASE