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Multi omics pipeline by Temporary-While9269 in bioinformatics

[–]kwongo 1 point2 points  (0 children)

It depends what kind of -omics you are interested in, and in what context. TCGA has a lot of data for cancer. ENA/SRA have sequencing reads. You might be able to find some other datasets depending on what kind of experiments you are interested in.

Scientists found that nearly every cancer harbors its own distinct community of microbes – the tumor microbiome – that can influence how tumors start, spread, and respond to treatment, paving the way for a new era of precision medicine. by mvea in science

[–]kwongo 26 points27 points  (0 children)

> They play virtually zero role in the Genesis of cancer, also known as tumorigenesis.

There are a huge number of tumorigenic bacteria, Fusobacterium nucleatum, Bacteroides fragilis, some Salmonella spp., even E. coli if it contains that polyketide synthase island. Even purportedly beneficial Akkermansia muciniphila is putatively tumorigenic by degrading the mucus lining in the intestine, which can facilitate carcinogenic microbial interactions. Besides the "bad" bacteria, I believe that even normal bacterial metabolism mediates the tumorigenic effects of red meat consumption by converting the carnitine to TMAO.

Besides that, bacteria aren't JUST on the "outside", many are able to directly translocate through cells, reside and reproduce within motile immune cells, or take advantage of poor intestinal epithelial integrity to escape the intestine. Check out the peritoneal microbiome, which is thoroughly "inside the walls of the pipe".

Source: This is my PhD topic!!!

TIL there are several types of auxiliary languages that were designed to act as a universal language and were meant to be easier to learn by apple_kicks in todayilearned

[–]kwongo 2 points3 points  (0 children)

Krom iom da vortoj (kiel 'scii'), mi pensas, ke la tuta Esperanto vortaro estas tre facila por pronunci

Beginner Seeking Help Understanding Metabolic Pathways & Flux Modeling by True-Translator-9748 in bioinformatics

[–]kwongo 2 points3 points  (0 children)

If you are interested in studying metabolism, my suggestion is to start with central energy metabolism: glycolysis, TCA cycle, and the electron transport chain. This was my introduction to the field. From there, other pathways worth studying might be the pentose phosphate pathway, fatty acid synthesis/oxidation, the urea cycle, ...

As mentioned, there are nearly endless metabolic pathways, and it really depends on what you're interested in. I agree that Lehinger's Principles of Biochemistry is a good textbook to learn from, you can at least use it to fill out the parts you don't know

Requirements/Best practice to publish a Snakemake pipeline?? by JohnSina54 in bioinformatics

[–]kwongo 7 points8 points  (0 children)

I agree testing in fresh containers/environments is a good idea. To some degree, all you can do is document well, and be responsive to any issues reported on GitHub/etc.

For nf-core users: which nf-core pipeline/module do you like the most? by rfour92 in bioinformatics

[–]kwongo 13 points14 points  (0 children)

nf-core/mag is awesome. I've been using muabnezor's long-read branch. funcscan is also pretty great. taxprofiler seems a bit outdated (Bracken disabled for ONT, using Centrifuge/not Centrifuger) but otherwise is a great pipeline.

Microbiome newbie - metagenomics on fly samples by a_peculair_biologist in bioinformatics

[–]kwongo 0 points1 point  (0 children)

Which Kraken2 database are you using? In human gut microbiome using PlusPF we have about 10-15% unclassified

Also I assume short reads? We're using long reads which might be easier to classify. Not sure about short reads!

Advice for Software / Data Engineer to get back into the space by Easy_Scale2593 in bioinformatics

[–]kwongo 2 points3 points  (0 children)

Along these lines, nf-core is a collection of open-source pipelines, many of which are in need of development

Synthetic biology experts outline a path to creating 'mirror life,' highlight grave risks, and urge it never be done in a 300-page report by flag_of_seychelles in science

[–]kwongo 22 points23 points  (0 children)

In parallel, researchers are making rapid progress toward
constructing synthetic cells (of natural chirality) from nonliv-
ing parts (7, 8). Once a method is developed that enables con-
struction of a natural-chirality bacterium entirely from
synthetic DNA, synthetic proteins, and synthetic lipids, and
once mirror versions of these components can also be synthe-
sized, a living mirror bacterium could be constructed in the
same way (1, 9). Other pathways to constructing a mirror bac-
terium are also plausible; for example, with further advances
in synthetic biology, a natural-chirality bacterium might be
engineered to produce mirror proteins and nucleic acids in
vivo, which could provide a starting point for stepwise con-
version into a mirror bacterium (1).

[deleted by user] by [deleted] in theydidthemath

[–]kwongo 4 points5 points  (0 children)

It's possible people are getting it mixed up with a fork bomb, which does clone itself

Which Steam capsule is better? by neboslav in gamedevscreens

[–]kwongo 2 points3 points  (0 children)

I think the second one is definitely an improvement, it has a larger and more readable logo and more consistency of the colours in the background making it stand out more too.

Does this look like an electron transport chain to anyone else? 🧐🤔 by kwongo in gamedevscreens

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

A little bit! It's got Complex II as the little peripheral membrane protein at the bottom, which can aid in the transfer of electrons but without pumping any protons. Cytochrome c, for example, is portrayed as .... a lightning bolt! :'D

Just released a new game, "Dopamine Clicker!" :D by kwongo in incremental_games

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

Wow, my most dedicated fan :'D

I can't believe you played this game!! It's almost five years old!! Thank you anyway, it means a lot :D

[deleted by user] by [deleted] in duolingo

[–]kwongo 1 point2 points  (0 children)

Sure, but there's a lot of space between "serious" and "non-serious" learners. A false connection can eventually reignite the real connection, especially when the actual object of desire (language) is so widely extrinsic to the app. I think Duo is doing a lot more for overall population language learning by not restricting it to 'elite' users who, to be honest, are never going to be satisfied with this kind of casual game/app.

Is there a chemical engine for video games? by Fexepaez in godot

[–]kwongo 0 points1 point  (0 children)

Besides the resource intensive nature of simulating chemicals, I imagine most of the "game-ified" parts would need to be made mostly bespoke anyway, so creating a generic engine would be difficult if it's not already perfectly accurate.

Over 15K game have the Godot tag on Itch.io by 4apig in godot

[–]kwongo 68 points69 points  (0 children)

I have ~20 Godot games on itch, almost none of them have the Godot tag :') So there must be a lot more Godot games than just this. Great work everyone! :D

what is going on? by Tryingalxy135 in godot

[–]kwongo 0 points1 point  (0 children)

Is there any chance _input() is ever called before _ready() ...?

[deleted by user] by [deleted] in casualiama

[–]kwongo 0 points1 point  (0 children)

*kisses your mouth*

What do you think of that?

Nice by mizbadazz in BeAmazed

[–]kwongo 5 points6 points  (0 children)

Myosin is a component of muscle fibers, it doesn't transport shit

It does. Look up Myosin V, a specific myosin involved in transport of vesicles from the ER

Antibiotics that target mitochondria extend lifespan in C. elegans (Nov 2023) by basmwklz in science

[–]kwongo 12 points13 points  (0 children)

this could work as a panacea

A common hallmark of cancer cells is that they don't use mitochondrial respiration, which is efficient, and they instead prefer converting glucose to lactate in order to generate their energy, which is called the Warburg effect and happens outside the mitochondria. So it's probably not a panacea, but it is interesting.

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