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Questions tagged [software]

Computer programs that aid in the storage, processing, and analysis of biological data.

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21
votes
4answers
837 views

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 ...
14
votes
4answers
651 views

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 ...
12
votes
2answers
317 views

Is there a program that simulates biology on a molecular level?

Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
8
votes
2answers
12k views

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? ...
7
votes
1answer
476 views

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 ...
6
votes
3answers
279 views

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]: ...
6
votes
3answers
4k views

3D models of adult male brain in the Blender software? Any open-sourced version for research?

I am trying to find 3D model of brains. I am particularly interested in adult-male -brains in Blender-model. I could find such 3D models of brains for sale here but because I am researching I would ...
6
votes
1answer
122 views

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 ...
5
votes
2answers
64 views

tools to reconstruct the transcriptional regulatory circuits?

What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?
5
votes
1answer
120 views

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 ...
5
votes
1answer
669 views

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 ...
5
votes
1answer
2k views

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 ...
4
votes
2answers
234 views

Is there a command line molecular cloning tool?

There are many softwares such as SnapGene, Geneious, Vector NTI, ApE, Gentle and others for assistance with cloning. Their key functions are: Making maps of plasmids Annotating plasmids with common ...
4
votes
1answer
626 views

Automatic cropping of collimated digital X-ray images

Do you have any suggestions for a library which offers an algorithm to crop digital X-ray images automatically? We receive full-size images (43x43cm) from a detector, independent of the collimator ...
4
votes
1answer
450 views

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 ...
4
votes
1answer
139 views

Online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology

Where can I find an online toolkit that provides functional similarity scores (in the form of a matrix) between two functional gene sets in the context of gene ontology? I have tried the following: ...
4
votes
1answer
1k views

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 ...
4
votes
1answer
2k views

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 ...
4
votes
2answers
363 views

Biological key file format

I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data. Thanks
3
votes
2answers
1k views

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 ...
3
votes
2answers
781 views

JMol “calculate HBONDS”: which atom is the donor/acceptor?

JMol can be used to identify Hydrogen bonds in proteins by the script "calculate HBONDS". By outputting the state of the network, we can obtain a lisdt of H-bonds. Here's one line from an example ...
3
votes
1answer
89 views

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 ...
3
votes
1answer
993 views

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 ...
3
votes
1answer
132 views

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 ...
2
votes
1answer
546 views

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 ...
2
votes
6answers
477 views

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 ...
2
votes
2answers
66 views

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 ...
2
votes
2answers
1k views

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 ...
2
votes
1answer
90 views

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?
2
votes
3answers
151 views

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 ...
2
votes
1answer
192 views

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 ...
2
votes
1answer
61 views

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, ...
2
votes
0answers
62 views

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 ...
2
votes
0answers
629 views

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 ...
2
votes
0answers
29 views

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 ...
1
vote
1answer
143 views

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 ...
1
vote
2answers
82 views

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.
1
vote
1answer
43 views

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??
1
vote
1answer
837 views

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 ...
1
vote
2answers
384 views

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. ...
1
vote
1answer
2k views

Is there a free alternative to Gelcompar for comparing banding patterns across multiple gels?

In order to run my microbial community samples from my experiments through DGGE, I was required to use multiple gels. Thus it is necessary to compare banding patterns across more than one gel. ...
1
vote
0answers
328 views

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 ...
1
vote
0answers
172 views

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 ...
1
vote
0answers
197 views

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 ...
1
vote
0answers
67 views

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)?
1
vote
0answers
224 views

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 ...
0
votes
1answer
76 views

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 ...
0
votes
1answer
89 views

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 ...
0
votes
0answers
12 views

Single cell lineage tracer

I need a Software or Python code or algorithm which can trace cell lineages. In my case the cells are budding yeast. I have already a segmentation python code and I only need to trace each cell.
0
votes
0answers
18 views

How to add taxa to a published tre file. What program to use? How to do it in Mesquite?

I need to add taxa to an already published tre file. (the Prum 2015 avian phylogeny). *For example if I wanted to add Western Gull to the tree (Larus occidentalis) knowing that Larus & Sterna are ...