Questions tagged [modelling]
Assignment of data into a defined mathematical description invariably associated with a priori assumptions
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Deseq2 model formula and longitudinal experimatal (or time-series) designs
At hand I have RNA expression data of 6 organs from mice with treated and untreated diets, collected at consecutive time points, and I wonder how to design an analysis accordingly in ...
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How to get Time-Course data for NOS2 & Arg1 Enzymes?
Background: I'm trying to model M1/M2 macrophage switch during a wound-healing process. For a switch from M1 cell population to M2 cell population, there is a reprogramming of the internal metabolic ...
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Finding persistence length using OxDNA on python
on OxDNA's documentation, i found a code for determining persistence length. However, i have ran simulations for different number of bases on OxDNA and have the following text file as results: Columns ...
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Cox model with percentage interpretation
Good morning,
I was wondering whether anyone could advice me on the following: I have a Cox survival model in R (function coxph), which ,among other variables (e.g. age, sex), contains a variable with ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
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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 ...
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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 ...
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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, ...
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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-...
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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 ...
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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 ...
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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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How I deal with this expression set?
I have a gene expression raw counts like below for 16 patients
...
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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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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 ...
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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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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 ...
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How I debug this code?
I am trying to run CMSclassifier::classifyCMSfunction on my data but I am getting this error
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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:
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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? ...
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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 ...
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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 ...
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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 ...
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