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Questions tagged [modelling]

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22 views

Profile HMM to find sequence motif using Baum-Welch instead of using a given multiple sequence alignment?

I know this can be very problem-specific -- but it seemed to me the standard approach to train an HMM to recognize a binding pattern of a protein is to use the multiple sequence alignment (MSA), ...
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1answer
46 views

How I deal with this expression set?

I have a gene expression raw counts like below for 16 patients ...
0
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0answers
47 views

Selecting genes with more contribution from PCA

I have RNA-seq data in response to treatment vs non response; By machine learning I selected three principle components likely can predict the response based on the gene expression. Now I have ...
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0answers
47 views

length of 'dimnames' [1686] must match that of 'dims' [3]

Please if anyone has experience with the use of the BSEQ-SC package for the deconvolution of bulk RNA sequencing data with single cell RNA sequencing data I will be very grateful for your suggestion. ...
3
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1answer
27 views

Does SBOL require representing intermediate products like mRNA?

Do I need to include intermediate gene products like mRNA in order to express a gene regulatory relationship in SBOL? For example, let's say that I'm representing transcriptional regulation of the ...
5
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1answer
53 views

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?
0
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2answers
62 views

Proteomics data Vs Transcriptomics data?

I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
0
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0answers
8 views

How to integrate the transcriptomics data with kinetic metabolic models?

I have created a convenience kinetics model. Now, I want to integrate the transcriptomic data with my convenience kinetics* model for altering/weighing the kinetic parameter values. I read some ...
-1
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2answers
118 views

How I debug this code?

I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error ...
2
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1answer
51 views

How to model the effect of acid/base on pH

I would like to model a biological compartment with sysBio R package. It is fine but I'm having a difficult time with modeling the change in pH due to acidosis. I tried several things like: ...
0
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0answers
57 views

Making a model of gene contribution in cancer diagnosis

I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders; I have done differential expression by DESeq2 and I obtained a ...
3
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1answer
38 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 ...
3
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1answer
174 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 ...
4
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1answer
74 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 ...
2
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1answer
72 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 ...
16
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3answers
663 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
107 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
107 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
155 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
119 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 ...