7 votes
Accepted

How to simulate biological pathways?

In matlab this can be done using the SimBiology toolbox. In mathematica this can be done using the SystemModeler. In python there are multiple packages, e.g. (in no particular order) PySB, Tellurium, ...
HasHPIT's user avatar
  • 86
6 votes
Accepted

What are the different kinds of bioluminescent genes?

There are three processes wherein light is emitted. Bioluminescence: a chemical reaction releases light. The enzyme that does this is luciferase, while its substrate is luciferin, a small molecule. ...
Matteo Ferla's user avatar
  • 4,234
4 votes

How can I translate infix to mathml using the python interface to libsbml?

It’s quite straightforward to convert infix to mathml using libsbml. Make sure you have libsbml installed in python by typing pip install python-libsbml at the ...
rhody's user avatar
  • 251
2 votes

What are the different kinds of bioluminescent genes?

The green protein is called GFP of 238 amino acid residues (26.9 kDa) and produced by: the jellyfish Aequorea victoria, It has a major excitation peak at a wavelength of 395 nm. the sea pansy, ...
M__'s user avatar
  • 12.3k
2 votes
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Software for microbial profiling from 16S rRNA gene sequence

I tried dada2 and is not bad (if you know R). QIIME2 is also an option. Many other are available, the choice might also depend on your sample and your exact question. For functional profiling you ...
Fabio Marroni's user avatar
2 votes

Weird phylogenetic tree

Anyway the chances are this is gene duplication. It will be a housekeeping type gene or else histone that sort of thing. You simply map the different genes onto the various metazoan classes. In your ...
M__'s user avatar
  • 12.3k
2 votes

Sophisticated algorithms in biological systems

There are many examples of biological systems doing computation, according to my understanding: Regulatory networks encode decision trees of significant complexity: wikipedia. Alan Turing did ...
Maximilian Press's user avatar
1 vote

Software for microbial profiling from 16S rRNA gene sequence

For comprehensive microbial profiling of your 16S rRNA gene sequence data from Illumina MiSeq, I recommend using the web app Microbioma16S (www.microbioma16s.it). This powerful tool offers an end-to-...
cami's user avatar
  • 11
1 vote

What are the different kinds of bioluminescent genes?

There appears to be a dinoflagellate with Luciferase and the diversity of their genes was studied in the Baltic, found described in an article here: https://www.tandfonline.com/doi/full/10.1080/...
TristanSC90's user avatar
1 vote

CRISPR screening and systems biology

To investigate genes through a network based approach you can use several tools. I don't know which level of programming you have or which tool you prefer but here is a brief overview of the ...
gabt's user avatar
  • 348
1 vote

CRISPR screening and systems biology

What do you call screening results? Do you have a kind of array with protein or RNA data? If so, you can use several open-source tools available on the internet, like Enrichr or network analyst to ...
FPS's user avatar
  • 87

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