Computer programs that aid in the storage, processing, and analysis of biological data.
9
votes
1answer
138 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?
5
votes
2answers
45 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?
4
votes
1answer
113 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
97 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
333 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 ...
4
votes
1answer
49 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
2answers
83 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
117 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
48 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 ...
2
votes
2answers
102 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
3answers
46 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
0answers
61 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 ...
1
vote
1answer
327 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
20 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
0answers
54 views
bam viewer that works on authenticated ftp urls with username/password combination? [closed]
Are there any BAM file viewers that will work on authenticated ftp urls with username/password combination?
For example, something like this:
...
0
votes
0answers
27 views
Modeller - Convert FASTA to PIR
I am doing a basic modelling following the instructions here. But different target / template sequences.
http://salilab.org/modeller/tutorial/basic.html
Do I need to convert the FASTA to PIR with a ...
