Questions tagged [systems-biology]

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running fragpipe

I am getting the following error when I run FragPipe on my Ubuntu machine 22.04 how do I fix this?
Mahendra Singh's user avatar
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1 answer

Sophisticated algorithms in biological systems [closed]

I am looking for examples of (known) algorithms/data structures in biological systems. My current understanding is that these don't exist - or haven't been found - beyond a relatively low level of ...
streawkceur's user avatar
1 vote
3 answers

Software for microbial profiling from 16S rRNA gene sequence

I have hundreds of GBs metagenomic 16S rRNA gene sequence data. I want to do microbiome composition profiling (with relative abundance) from the data. Also after that, I will do functional profiling (...
DEEP's user avatar
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4 votes
3 answers

What are the different kinds of bioluminescent genes?

I know of the common green glow gene but I forgot the name and I also know that some algae glow blue. There are so many types of bioluminesent organisms, so I am wondering what species have which ...
TristanSC90's user avatar
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2 answers

CRISPR screening and systems biology

I am not sure how to tackle this one, so I’ll explain the general idea I have in mind. Given results of a CRISPR knockout screening experiment (like in this paper) with two types of assays: control ...
0x90's user avatar
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1 vote
1 answer

Weird phylogenetic tree

I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search. ...
Zaci's user avatar
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6 votes
1 answer

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

Assume I have an infix expression such as k1*s1, how do I use libsbml to translate this expression to mathml using the python interface?
rhody's user avatar
  • 251
3 votes
1 answer

How to simulate biological pathways?

I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using Control Theory. Is there a standard way to simulate pathways by using ...
0x90's user avatar
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