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17

There is a recent paper that introduced the first molecular-level whole-cell simulation. Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 DOI: 10.1016/j.cell.2012.05.044 The ...


9

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 ...


9

ImageJ is all you need. Particularly see the documentation sections on setting the image scale and measuring.


6

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 ...


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

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

There is a lot of variation in how and when deer shed their antlers. In most arctic and temperate-zone species, antler growth and shedding is annual, and is controlled by the length of daylight. In tropical species, antlers may be shed at any time of year, and in some species such as the sambar, antlers last several years. Some equatorial deer never shed ...


3

At the MEME server page, there's a link to upload a customized background markov model (using the command line interface, this is the -bfile option). From there, there's a link to the MEME Man Page. Under "Objective Function", it specifies: The background model is an n-order Markov model. By default, it is a 0-order model consisting of the ...


3

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 ...


3

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.


3

Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools do exist, I doubt ...


3

I also had to do the same using Jmol, and I figured it out how to get a list of all the hbonds. Step 1: Calculate the hbonds with or without RASMOL method. It's up to you, e.g., jmolScriptWait("select not hydrogen; set hbondsRasmol FALSE; calculate HBONDS") Step 2: Only display the hbonds jmolScriptWait("display connected(hbond)") Step 3: Export the ...


3

I dont know about JMol, but this can be easily done with UCSF Chimera. I loaded the 1a1x structure. Then selected: Tools > Structure Analysis > FindHBond I kept the default values and selected Write information to reply log Then clicked OK On the structure the H Bonds will be identified with a coloured line. To view which is the donor and acceptor go ...


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 ...


2

I think that you could try a similar approach to GSFS: use transduction in proteins (if you don't know star code, then you must use 3 strings for each gene) use a basic tool (a stand alone like UNIPROT tools) to identify the proteic domain type (chain alpha, ..) divide the genes by proteic domain type (pdt): which contains which pdt and the pdt order ...


2

One application that I am aware of that will do this, as well as much else besides, is Swiss-PDB Viewer aka DeepView. If you go to the site and select User Guide in the left hand tabs you will see a subsection called mutations and following that will tell you what the application can do.


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

http://www.turbosquid.com/3d-models/max-human-brain/580672 That one is only 30 which really isn't bad for a model. You will have trouble finding an anatomically correct model for free. I am curious, is the male brain that much different from the female brain? And do you want just the brain or a whole head with the skeleton and other anatomical features? ...


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

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

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 ...


1

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.


1

I would recommend Galaxy. https://usegalaxy.org/ The system does include primer design, sequence alignments and covers many common bioinformatics tasks.


1

I would go for StrainControl Laboratory Manager. Works perfect and covers all needs of a lab. Do not go for all the "free" stuff since they rely on a active sponsor and your data is never safe.. StrainControl is free for 3 months and if you want to continue use it you simply purchase the Admin password and all your data is saved. Check it out at ...


1

WebPlotDigitizer is an online application that can also be used to make distance and angle measurements in an image.


1

Try this out with BioPython: from Bio.PDB.PDBSuperimposer import PDBSuperimposer as superimposer from Bio.PDB.PDBParser import PDBParser parser = PDBParser() sup = superimposer() struct_1 = parser.get_structure("XXXX","first_pdb") struct_2 = parser.get_structure("XXXX","second_pdb") atoms1 = struct_1.get_atoms() atoms2 = struct_2.get_atoms() ...


1

After you load the molecule in VMD, from the menu bar select Graphics->Representations... In the box labeled Selected Atoms, type "hetero" and hit enter. You should now see only your ligand (and whatever other non-protein/DNA atoms that happen to be in your PDB file). Hit the Create Rep button, enter "protein" in the Selected Atoms box and hit enter (you can ...


1

The Open Source Computer Vision library OpenCV is pretty popular. I'm a Python guy, but it also has C, C++, and Java interfaces. The O'Reilly book Programming Computer Vision with Python was pretty good, and their C-oriented Learning OpenCV from 2008 is coming out with a new C++ edition in July, supposedly. There are also the OpenCV online docs, linking to ...



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