13 votes
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Computer Virus that infects DNA?

As I understand from your post, the computer virus you are talking about is modifying database (FASTA files) in genetics. That would have a pretty bad impact on research in genetics and medicine. If ...
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  • 67.7k
10 votes
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What is the best file format to store gel images?

Always keep the raw data files! This is always a good idea for scientific data, and the only exception should be if the raw data is prohibitively large and it is not feasible to store it completely. ...
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7 votes
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Programs/software to graph biological data

There is no standard software, programming language, or library used for computing and graphing biological data. The R language is commonly used for statistical work, but Python (in conjunction with ...
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7 votes

Machine learning for light microscopy -- problems to solve?

I know this question is going to close. But, if you want to work something you can work on: Cryo super-resolution fluorescence imaging Highlights CryoFM allows imaging of vitrified ...
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5 votes

How to retrieve full gene names list and Entrez gene IDs and other annotation information from HUGO gene name list (in R or any)?

I would recommend just downloading the database, which HUGO allows you to do free of charge. The HUGO website has a "downloads" tab at the top that takes you to the following page http://www....
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  • 6,169
5 votes
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What Software could I use to create Diagrams of Biochemical Processes like these?

By posting to this forum, I presume the question is whether the illustrators of this and other biochemistry books used software specifically designed for the purpose of drawing reaction pathways, or, ...
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  • 22.5k
4 votes

Machine learning for light microscopy -- problems to solve?

RE: What kind of software you always wanted for light microscopic research, but did not know how to build? I research fruit flies and in this field (and many other insect ecology model systems like ...
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  • 16k
4 votes

Is there a command line molecular cloning tool?

Making maps of plasmids Annotating plasmids with common features Plasmapper works through commandline Finding restriction sites Simple regex searches can do that Mapping Sanger sequencing ...
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  • 35.1k
4 votes

What Software could I use to create Diagrams of Biochemical Processes like these?

In the scientific community, we mostly use a couple tools to draw publication-quality pathway figures: OmniGraffle BioRender These tools are optimized for making the kinds of figures shown in your ...
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3 votes

How to generate protein graphics for illustrating articles?

All comments are great, there are numerous software programs that allow you to make such images. Gathering information about the insulin structure By simply clicking on the image in wikipedia it ...
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  • 2,340
3 votes

what is the principle behind Allele Frequency Net Database

Allele frequency is simply the frequency at which a specific allele is found in members of a population. Let's take the following example from the site you referenced: The first column merely has the ...
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3 votes
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curly braces in sequence motifs

N is the IUPAC code for any nucleotide, so in DNA sequence an N signifies any one of the four bases could be in that position. The {4} means 4 of the previous character in the pattern, or NNNN. In ...
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  • 3,432
3 votes

Is there software or a website where I can browse extinct species?

You can search for species that are "Extinct" or "Extinct in the wild" at the IUCN red list website (International Union for Conservation of Nature and Natural Resources). That list currently includes ...
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3 votes

What (open) software there are for simulating behaviour of human (cortical) neurons?

No, not in the neuronal level. Because IMHO this is an ill-posed problem. EEG combined with MRI won't have the resolution to do solve the inverse problem of neuronal network simulation. There are at ...
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  • 3,045
3 votes

Software for counting fly eggs

ImageJ is a multi platform piece of software that has a cell counter module that might be of some use, and hey its free! Its easy to use and so ludicrously crude that it is very versatile. I remember ...
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  • 11.3k
3 votes

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

There is a model of an adult, male, real human brain here: http://brainder.org/download/brain-for-blender/ It can be imported into Blender or any other 3D application that can read Wavefront OBJ or ...
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  • 31
3 votes

What Software could I use to create Diagrams of Biochemical Processes like these?

I have used Draw.IO for similar tasks involving flow charts from scratch. I've also used Adobe Illustrator, usually to modify figures when I have them in a compatible vector graphics format. Finally,...
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  • 36.7k
2 votes

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

NAMD is a molecular simulation software system with an extensive, active community of researchers https://www-s.ks.uiuc.edu/Research/namd/ it has a slick visualization package called VMD https://...
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2 votes

Software to calculate Fst from sequence data

If You are familiar with R, try package adegenet. It contains very nice tutorials explaining its usage, including the very R basics. If You require graphical interface, install RStudio - very nice ...
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  • 101
2 votes
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Visualisation of phylogeography

I think Spread will be best for this work. SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics Authors: Filip Bielejec, Andrew Rambaut, Marc A. Suchard & Philippe Lemey ...
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2 votes

Machine learning for light microscopy -- problems to solve?

One of my colleagues does lots of histological work, staining and identifying tissue at the microscopic level. Software that could be helpful to that discipline might be the ability to distinguish ...
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2 votes

Machine learning for light microscopy -- problems to solve?

You might be interested in reading the article "Machine learning in cell biology – teaching computers to recognize phenotypes" (http://jcs.biologists.org/content/126/24/5529.long)
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2 votes

Computer Virus that infects DNA?

This is very silly. All the computer virus is doing is corrupting a text file in a computer database. If someone uses the information in the corrupt file to synthesize actual DNA to modify a living ...
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  • 22.5k
2 votes
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Is there a free software for manual sequence annotation?

You might find some success with using WebApollo or JBrowse WebApollo allows you to perform many manual annotation functions for your genes, such as editing exon boundaries, fixing coding sequences, ...
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  • 166
2 votes
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Mouse Colony Software

Here is a list of programs that could work: E-mouse Lab: http://e-mouselab.com, seems like the best fit for your requirements. ZooEasy: http://standalone.zooeasy.com/en/pedigree-software/breeding-...
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  • 3,069
2 votes

Neuro-simulation tools

Another option, maximal in terms of flexibility albeit also possibly effort, is to write your own. Of course, this presupposes some extra knowledge. However, I think coding your own gives a level of ...
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2 votes

Neuro-simulation tools

I have only used NEURON and the DIY approach for small scale simulations. You can have a look at this comparative table: https://grey.colorado.edu/emergent/index.php/...
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  • 1,189
2 votes

Significant presence/absence of plant species

I am not quite sure what you mean by "significant presence". If you observe any non-zero number of plants of a given species in a cluster, then the rate at which this plant occur in this cluster is ...
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  • 67.7k
2 votes
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What software do I need to read-write cas9? and .dna files?

You have a long journey ahead. This guy spent about 4 years to learn what he is doing here. He is using Snapgene software
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2 votes

Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?

Have you ever tried using Mesquite? I used it when I taught intro bio lab course as a TA. Basically you try to come up with yes or no questions, and based on how you answer these questions it will ...
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