Questions tagged [software]
Computer programs that aid in the storage, processing, and analysis of biological data.
58 questions
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Why isn't all genetics work published on GitHub?
Update: When hackernews is ruthlessly critical of a new software project, the implicit assumption is that software projects are dime-at-dozen, attention of HN users is worth millions of dollars, hence ...
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What software can be used for simulating human meiosis, taking linkage and recombination into account?
I want to study the nature of genetic variation in offspring from the same set of human parents. To this end, I would like to take two (male and female) complete genomes, generate gametes from them, ...
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Is there no good way to run the Vienna RNA tools on Windows?
I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, ...
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Is there any bloodstream chemical composition software simulator?
Let's say I'd like to know how certain substance affects bloodstream levels of certain drug during a period of time. Is there any simulation software available publicly to run such kind of simulation?
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Interactive molecular machinery visualisation software?
If I want to manually feed mRNA through a ribosome to actually see what happens step by step which software can I use to do that?
I'd like to be able to see changes in geometry and orientation at an ...
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3
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What Software could I use to create Diagrams of Biochemical Processes like these?
Cross-posted at GraphicDesign.SE here
Is there any software software that I could use to (closely) create pathways as depicted in these diagrams?
Or does anyone happen to know what software ...
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Is there any free software similar to CellDesigner that allows me to represent large networks of biochemical reactions in the human body?
I continually have to review multiple articles, in multiple journals. These articles present how various enzymes, proteins, lipids, carbohydrates, etc. intervene in the processes that lead to certain ...
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Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?
I asked a similar question on Quora before, but did not get any useful answers as the program the one answerer suggested turned out to have the exact same problems as all others I have found so far.
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1
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What software do I need to read-write cas9? and .dna files?
I am still a complete beginner to crispr and I am still trying to learn what it is and how to actually use it. I now realise that you have to order the crispr components after you have actually ...
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2
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1
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How to generate protein graphics for illustrating articles?
The structure of insulin shown below appears in a Wikipedia entry.
What software was (or can be) used to create pictures of this type?
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Is there human Anatomy software that provides great detail?
Is there Anatomy software that is exact representation of human body, like let's say virtual reality tour inside human body from head to foot, detailing all organs even small, covering all systems, ...
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Neuro-simulation tools
I know, this question is opinion-based, but where else should I ask it (or how could I ask it here without being flagged "opinon-based!")?
Which neuronal simulators - in the line of NEURON and ...
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346
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What is a proper software to do GWAS analysis of tuberculosiis VCFs and phenotype data?
What is a proper software to do GWAS analysis of tuberculosis VCFs and phenotype data? Need a software which will accept VCF file and phenotype data as an input and produce genome wide association ...
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138
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Significant presence/absence of plant species [closed]
I have approximately 300 cluster of 200 different plant species and a presence absence matrix of all species versus clusters (since some species don't have clusters so they are checked if they are ...
user28219
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71
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Phylogenetic tree with tagging
I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
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User friendly phylogenetic tree editing software
Background: I have Hackett 2009 (from birdtree.org) phylogenetic tree and I need to reorder it according to Prum 2015. I also work only with some species relevant to my project, not the entire tree.
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Computer Virus that infects DNA?
I have watched a talk by Mikko Hypponen (CEO of the security company F-Secure) called Silicon Plague. There, roughly at minute 51 of the talk, he mentions a computer code that is supposed to be able ...
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Do blurry images cause eye strain? At what point is an image so blurry the eye stops trying to focus it?
I'm a user experience designer concerned about a new trend of blurring screens when showing a lightbox/dialog box over top (see below).
From what I know, blurry images cause the brain to work hard ...
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Is there software or a website where I can browse extinct species?
Is there any software/website where I can browse for extinct species? It must be based on real animals that are now extinct. It may be in animated versions.
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776
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Programs/software to graph biological data [closed]
I am curious about what sort of programs people in my field of academia are using to graph their data. I am a master student in biochemistry, and have more or less only used excel (on rare occasions I ...
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what is the principle behind Allele Frequency Net Database
I just wanted to know what is the basic principle of Allele*Frequency Net Database. How are the frequencies present in them calculated??
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152
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curly braces in sequence motifs
what do curly braces in sequence motifs stand for?
e.g. in
RTCRYBN{4}ACG
what is N{4}? moreover, i notice that in TRANSFAC ...
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2
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1
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254
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Is there a free software for manual sequence annotation?
I'm looking for a software that would allow me to make a quick graphical annotation of the structural features of a sequence. Something that would look like what you get in jalview, with your sequence ...
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5
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1
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2k
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Mouse Colony Software
I am looking for a good mouse colony census program that tracks the mice we have in the lab, breeding success of breeders, lineages, multiple user access, etc. Jackson labs has a program that does ...
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186
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How to do Sliding 80mer Window search against a database with fasta
I know how to do a 80-mer window search against a single protein
...
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What (open) software there are for simulating behaviour of human (cortical) neurons?
Is there any reliable open-source software for simulating the behaviour of human cortical neurons? I am looking for serious software, so let's assume I have access to a computer with more than 10,000 ...
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0
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What software/approach to use to build a graph based on microarray gene expression correlation?
What software to use to build a graph based on microarray gene expression mutual correlation?
I have tried Cytoscape`s Reactome FI and a recipe from R bioinformatics cookbook, however, need a more ...
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2
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1k
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How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?
How to retrieve full gene names and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any other software or language)?
Is it possible vice versa: having full gene ...
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0
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260
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How do I import FASTA files into Haploview?
I'm trying to produce a haplotype network and so have decided to use the software haploview. However I'm having some problems importing my sequences into the software.
I Have my sequences in a FASTA ...
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3
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Is there a command line molecular cloning tool?
There are many software applications such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are:
Making maps of plasmids
Annotating plasmids ...
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2
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0
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71
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Open Source Variant Caller comparable to GATK Haplotype Caller?
Is there a Variant Caller comparable algorithmically and in performance to GATK Haplotype Caller but Open Source Compliant (non-restrictive use)?
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4
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959
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Machine learning for light microscopy -- problems to solve?
I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The ...
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Software to calculate Fst from sequence data
I'm looking for a software to calculate Fst from 3 loci DNA data of individuals from a metapopulation. I don't have any prior on the population structure (have no idea of the number of subpopulations ...
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What is the best file format to store gel images?
I store many gel images which are included in my Latex notebooks. The geldoc software normally produces TIFF files, however, Latex only accepts PNG or JPEG.
If I am going to store only a single copy ...
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3
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How can I re-format my DNA motifs' position weight matrices?
I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites).
The motifs belong to several species, and I wanted to cluster these ...
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146
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Visualisation of phylogeography
I am working on phylogeography on one model species and I am a beginner. You can imagine one species that came on locality more than 5 mya (million years ago). It was a good environment, so the ...
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6
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Sequence analysis software suites
I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what ...
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For people who work in microbiology labs, what software do you use to manage your strains?
It's just a small microbiology lab that currently records everything on paper, and there's quite few mutants as well. Is Excel commonly used for this sort of thing? Or is there a better software to ...
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3
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How easy is it to carry out de novo sequence assembly?
Today a colleague of mine asked the following question:
" Assuming I need to build from 0, a chromosome of a fish, with short reads
but no other reference whatsoever [de novo assembly]:
how ...
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What are the differences between HPRD and BIOGRID databases?
What are the differences between HPRD and BIOGRID protein-protein interactions databases?
What are their purposes? Why do we need two different databases?
How is data collected into each one?
How ...
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0
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235
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Workflow for batch analysis of ROI in histology samples
This is a pretty big task, and I have several work-arounds, but I am looking for an efficient way to go from PAS stained slides of lung tissue to defined ROI's over the whole slide (presumably via ...
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2
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Free software for measuring parts of an image? [closed]
Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? ...
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1
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1
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Statistical Analysis of Protein Folding Problem [closed]
I’m new to the field of protein folding. I’ve been searching and came across some books for predicting structures (Introduction to Protein Structure Prediction: Methods and Algorithms). Does anyone ...
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144
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Superposing DNA
I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used.
I can ...
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How does MEME compute the background frequency of nucleotides?
I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested.
I would like to know how MEME estimates the background ...
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4
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How do I view the simulated protein structure along with ligand in VMD?
I did a simulation of a protein-ligand complex, and it has stabilized after 5 ns. I have got the respective pdb files for every ns, but when I try to view in VMD (Visual Molecular Dynamics), I cannot ...
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Software for counting fly eggs
Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...
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2
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2k
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What would it take to recognize a deer by its photo?
I am trying to recognize a deer by its antlers or any other means.
Elaborating:
I was hoping to use their antlers to recognize them but I have heard that most deers shed their antlers every year so ...
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0
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Do the antlers re-grow in the same pattern every year? [duplicate]
I am a software engineer and I am trying to develop a system to identify a deer by its photograph.
Most deers lose their antlers every year. I would like to know if they re-grow in the same pattern ...
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3
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What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?
I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
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