Questions tagged [systems-biology]
The systems-biology tag has no usage guidance.
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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?
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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 ...
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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 (...
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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 ...
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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 ...
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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.
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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?
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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 ...
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