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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 one uses such a database to synthesize/edit sequences and then introduce this DNA into a living organism, then yes the computer virus would have affected a ...
11
ImageJ is all you need. Particularly see the documentation sections on setting the image scale and measuring.
10
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. This is not the case for gel images, so I would always keep the originals, and then use a cropped and edited copy in a suitable format for documents.
The ...
7
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 biological samples with fluorescence microscopy.
There are significant challenges to achieve high-resolution cryoFM imaging.
Fluorophore characteristics at low ...
7
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 the SciPy stack) and C++ also gets used a lot.
Before going further, I should point out you are asking two questions. One about computation and the other about ...
5
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.genenames.org/cgi-bin/statistics
You will see a table of statistics relating to how many protein- or non-protein-coding genes there are catalogued, etc.
Under the ...
5
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, if not, whether such software exists. From my experience of using such illustrations in my own teaching over the years, I believe that the answer is probably no ...
4
One of the quickest ways to get oriented on what is going in the world of protein folding and modeling is to look at the proceedings of the Critical Assessment of Structure Prediction (CASP). CASP is basically a contest, held every 2 years where anyone can use their algorithm to predict the 3D structure of a protein whose structure is known, but not ...
4
You can try looking around biostars.org, which is like stackexchange, but for bioinformatics.
Velvet is one example of a de novo assembler.
But 30 bp is really short, and animals have big genomes (not as tough as lots of plants and fungi, but still tough)
What you would get is a bazillion short contigs. It would not be pretty.
4
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 beetles, moths, butterflies) we use a lot of visually scored data, e.g. body size, wing size, wing morphology, eye colours, bristle numbers, genital morphology,...
4
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 question.
Others have also used Adobe Illustrator, Inkscape, or PowerPoint.
Like OmniGraffle, Illustrator and Inkscape can export resolution-independent ...
3
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 least hundreds of thousands of neurons that would be involved in your specific behavioral task, and you have at most a few hundred electrodes. You'll have to ...
3
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 reads
BLAST will do it.
Showing sequence, reverse complement of the sequence, translations in
different frames
EMBOSS has a collection of tools for these ...
3
I would strongly recommend benchling https://benchling.com
This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently ...
3
If you only want to use only sequencing techniques, you have a problem.
To get a feeling of what kind of results to expect, consider this paper published recently in Nature Genetics. They tried to assemble a whale genome de novo. They had 7 (!) paired-end libraries with different insert lengths ranging from 170bp to 20kb. Read lengths were mostly 100bp and ...
3
So what you need is basically your data expressed as counts instead of proportions. Even if you do not have the matrix of counts as raw data, these proportions only needs to be multiplied by the total number of binding sites used in the study (e.g. the number of sequences that have been analysed) to get the counts (since proportion = count/total number of ...
3
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 using it in undergrad to count cells under the microscope automatically after a few image contrast tweaks. I don't see why this couldn't be reapplied to count ...
3
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 Stanford PLY formats.
3
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 Perl regular expressions \d{4} means match 4 digits in a row, so the notation is quite similar.
3
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 name of the allele, A*01. The second column is the population from which individuals were genotyped. Skipping ahead, the fifth column is the number of people ...
3
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 903 species, but some of the assessments might be obsolete (see annotations). From that list, you can click and get some basic information about each species.
...
3
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 will provide you with valuable information:
Created by Isaac Yonemoto created with en:pymol, en:inkscape, and
en:gimp from NMR structure 1ai0 in the en:pdb....
3
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, I've often made similar graphics directly in PowerPoint when I needed them only for a slide presentation and not a paper-quality figure.
As @David mentioned, ...
2
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://www-s.ks.uiuc.edu/Research/vmd/
2
Short Answer
In a nutshell, there are two major differences:
Species range: BioGRID integrates multiple species' protein-protein interaction (PPI) data, whereas HPRD focuses mainly on Human data.
Functionality: HPRD has some GUI tools that can interact directly with it's database (e.g. BLAST - for searching proteins and their binding partners via sequence ...
2
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
Homepage: http://www.phylogeography.org
License: LGPL
2
I personally use more frequently Geneious for most of the basic every-day manipulations (my university bought a license), but I would recommend Ugene: it's free, open-source, cross-platform and supports batching and scenarios.
2
I really like the genious software suite. It can multithread and really use the performance of your computer. Even complicated things like De Novo assembly are very very intuitive.
2
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)
2
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 front-end for R. There are more possibilities how to calculate Fst in R, but adegenet is one of the most powerful genetic packages there.
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