Questions tagged [modelling]
Assignment of data into a defined mathematical description invariably associated with a priori assumptions
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questions with no upvoted or accepted answers
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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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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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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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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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1
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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.
...
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Interlink among different length scales of simulation and modelling techniques
I found this figure
in the following paper
A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites
However, I am skeptical about its correctness, as this paper is not peer-...
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GSM Modelling Issues. Problems replicating results during FBA/FVA Optimization
recently I've decided to start learning about GSM and I am currently applying them to a practical scenario of cyanobacteria metabolic engineering.
I am trying to perform FBA and FVA analysis of a ...
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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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