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Questions tagged [modelling]

Assignment of data into a defined mathematical description invariably associated with a priori assumptions

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1 vote
1 answer
108 views

Single or partitioned model for supermatrix tree inference?

I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
0 votes
0 answers
17 views

Why don't we use a multivariate (all genes) model for differential expression analysis?

Why differential gene expression analysis (counts) is done with multiple simple models, each with one single gene? Why not one multivariate model with all genes simultaneously? I mean a linear model ...
2 votes
1 answer
104 views

Model optimization causes overfitting

I'm working on an ML model to predict colorectal cancer using data from the human microbiome (collected from fecal samples). My dataset is made up of metadata (containing phenotypic information on the ...
3 votes
0 answers
31 views

How to do post hoc comparisons after a repeated measures ANOVA in R

I have a data set of several samples with their expression of proteins, in response to four different doses of a drug and two genotypes. I have been able to generate the two-way ANOVA using ezANOVA ...
2 votes
1 answer
35 views

Can you recommend me some programs or R packages for species distribution modelling?

I am working with a whole genus of land snails, trying to predict its distribution in the coming decades and how it might get affected by climate change. I have already worked with MaxENT and the R ...
3 votes
2 answers
820 views

Determining significance of a variable in a glm model

How would one determine the significance of a variable in a glm model? If I, for example, have a dataframe like the one seen below, how would I determine if the origin of the sample has a significant ...
1 vote
2 answers
93 views

Advise on building an effect ML model for predicting important proteins for drug response

I want to create a model to predict proteins which could be associated with drug response in cancer cell lines. I have cell line proteomics data, with compound screening data they have gained for a ...
0 votes
0 answers
8 views

Where would I get the activity profile dataset for Lantus Solostar insulin, and for other diabetes treatments such as Metformin?

I am working on a personal project for a better, more informed management of my own Diabetes Mellitus, Type 2 (aka "T2DM", or "T2D"). With some difficulty I am able to access and ...
3 votes
1 answer
70 views

How to prove correlation between gene expression and functions using omics data in bioinformatics?

I am new to bioinformatics, coming from a background in mathematical biology. I am currently participating in a project where the Principal Investigator (PI), who is a biologist, has tasked me with ...
3 votes
1 answer
106 views

how to add a custom elements into PyMOL visualization?

I would like to add some 3D elements (balls and lines) to the PyMOL visualization to highlight some "holes" in the structure. Say I fetch 1tqn and I want ...
-1 votes
1 answer
103 views

What are the fastest way of feature selection in R for large dataset in Machine Learning?

I have about 100 data sets with over 100,000 rows and 27 predictor variables and multiple response variable on each dataset. I want to select the most essential Features for these datasets. I used ...
0 votes
1 answer
294 views

How to use multiple .pdb files as templates for homology modelling?

I just ran an AlphaFold job for PduK from the Pdu BMC operon and got very strange results including a large circular loop of random coil. According to Mayer et al., PduK should be semi-triangular ...
4 votes
1 answer
195 views

Comparing phylogenetic models with different datasets

I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...
0 votes
1 answer
31 views

Would duplicate climatic variables impact maxent?

I want to use maxent to make some future distribution predictions. I downloaded future climate data from worldclim. In worldclim's page there are three variables (max temp, min temp and precipitation) ...
5 votes
3 answers
2k views

Why can't AlphaFold predict the consequences of point-mutations?

In the literature, it specifically states that AlphaFold has "Has not been trained to predict structural consequences of point mutations". See : https://alphafold.com/faq AlphaFold has not ...
2 votes
0 answers
11 views

Flux balance Analysis, Result interpretation, solver Solver Heuristics

i am new to modelling of cellular networks, and I have two basic questions, regarding the result interpration. I am using the COBRAToolbox to do a flux balance analysis of a whole genome scale model ...
2 votes
0 answers
40 views

What is coarse-grained modeling of proteins?

I need beginner-level study materials for coarse-grained modeling of proteins. Can anyone supply me with entry level resources besides the Wikipedia article? Background Coarse grain protein modelling ...
5 votes
2 answers
532 views

How do I build a glycosylated protein from PDB files manually?

I have a large protein PDB file (~3500 residues) and a couple of PDB files containing glycan structures I sourced from GLYCAM. How can I attach the N and O-glycans onto each protein residue with ...
0 votes
1 answer
279 views

NMF clustering not giving results

I'm trying to run the Non-Negative Matrix Factorization(NMF) for my Gene Expression dataset which was originally in matrix form. But it throws errors as given below: ...
1 vote
1 answer
76 views

Visualizing cell growth

I model the following events: a rod-shaped cell with center $x$ grows symmetrically until it reaches a maximum length/age, it divides into two identical cells, and the process continues. At division, ...
2 votes
1 answer
126 views

Tools for modelling and visualizing growth of cells

I am looking for a program/GUI app/package that would help me do simulations for cell growth. I have a microscopic mathematical model, and the scenario is basically the following: I start with a rod-...
4 votes
1 answer
239 views

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

There are wet methods: Patient-derived models: Patient Derived Xenograft (PDX) and Patient Derived Organoids (PDO) to reflect tumor biology. Are there any databases or computational tools that use ...
1 vote
0 answers
51 views

Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
2 votes
0 answers
48 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), ...
0 votes
1 answer
63 views

How I deal with this expression set?

I have a gene expression raw counts like below for 16 patients ...
0 votes
0 answers
246 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 ...
6 votes
1 answer
108 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?
3 votes
1 answer
43 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 ...
0 votes
2 answers
274 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 ...
-1 votes
2 answers
360 views

How I debug this code?

I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error ...
22 votes
3 answers
2k 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 ...
2 votes
1 answer
61 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: ...
3 votes
1 answer
55 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 ...
4 votes
1 answer
82 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 ...
4 votes
1 answer
1k 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 ...
2 votes
1 answer
98 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 ...
5 votes
0 answers
259 views

Differences between TM and GDT-TS scores for structure comparison [closed]

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 votes
1 answer
127 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 ...
9 votes
1 answer
162 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 ...