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Questions tagged [modelling]

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16 views

Can I calculate maximum parsimony for a binary dataset with morphological characters?

I have a dataset with binary morphological characters. I am wondering if it is possible to calculate the maximum likelihood of a phylogenetic tree for this dataset, but it seems that all of the ...
3
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1answer
31 views

Is there any tools that can generating FBA model from genome sequences or proteome sequences?

Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them? What I was thinking is more like to ...
2
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1answer
60 views

Hierarchical models with limma?

I have a dataset with (microarray) gene expression data that was sampled from the same individuals at multiple timepoints. Our exposure is a continuous variable, and because this was an observational ...
5
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1answer
68 views

How to verify if the stationary states of a biological model are correct?

I'm mathematically modeling yellow fever, and yet, after assembling the model, I need to find the stationary states of the model. I had to do it by hand because wolfram software could not get the ...
1
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1answer
49 views

Link Prediction in Bipartite Networks between biological pathways and drugs

Currently I'm building a big matrix (using microarray, mass spectrometry, RNAseq data) that consist by pathways (rows) and treatment/drugs (columns). The values of that matrix are scores that ...
14
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2answers
177 views

What is the actual cause of excessive zeroes in single cell RNA-seq data? Is it PCR?

First, sorry if I am missing something basic - I am a programmer recently turned bioinformatician so I still don't know a lot of stuff. This is a cross post with a Biostars question hope that's not ...
4
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0answers
51 views

Differences between TM and GDT-TS scores for structure comparison

What are the relative advantages / disadvantages of the TM (template modelling) and GDT (global distance test, total score) scores, used in protein structure prediction competitions, such as CASP? ...
0
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1answer
98 views

Mathematical notation for formulating a rank score

This is a cross-post from Mathematics forum. As no one has answered it yet, I fIgured post here as well. I would like to describe a transform I used to rank my data points. I have recoded my variable ...
3
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1answer
117 views

How are PDO and PDX used in computational and predicative models for tumour biology?

There are 2 new wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases/resources/computational ...
9
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1answer
110 views

Expected allele frequency distribution of SNVs in real NGS data

I have a huge amount of ~20x human WGS samples, aligned, and all SNVs that were called with GATK under standard germline parameters set. What I need to do is to model SNVs Allele Frequency (AF) for ...