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DOAJ (Directory of Open Access Journals)

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DOAJ (Directory of Open Access Journals)

DOAJ is a community-curated online directory that indexes and provides access to high quality, open access, peer-reviewed journals. DOAJ is independent. All funding is via donations, 40% of which comes from sponsors and 60% from members and publisher members. All DOAJ services are free of charge including being indexed in DOAJ. All data is freely available.
DOAJ operates an education and outreach program across the globe, focussing on improving the quality of applications submitted.

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Journals and their articles are categorised using a subset of the Library of Congress Classification. You can either type a keyword into the box below or click the arrows in the tree to expand and collapse subjects. Clicking on a subject will reveal the number of available records in the box on the right.

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How to keep chain ID / IDs in GROMACS?

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In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f  xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]
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GNUPLOT: How to draw trend line?

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How to draw trend line in the GNUPLOT? If you like to plot graphs in gnuplot and dont know how to plot trendline then here you are. Follow the steps mentioned below... 1. You should have a files with X and Y values 2. Open GNUPLOT (Operating system dosen't change anything here. It works on all systems) 3. Type the command in the gnuplot terminal Lets say I have a file for eg. '1.txt' p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth acsplines title '1.txt' OR p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth bezier title '1.txt' It will plot as below...
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MD convert (xtc to dcd)

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CATDCD program can be used to convert one file format to another file format. For example: How to convert trajectory output of GROMACS .xtc format into NAMD .dcd format ==== /path/to/catdcd -o /path/to/save/file/abc.dcd -xtc /input/path/to/save/file/abc.xtc ==== How to install CATDCD? Follow the link-   https://www.ks.uiuc.edu/Development/MDTools/catdcd/ Download the catdcd-X.Xx.tar.gz Extract all files from the tar. Locate the catdcd file. It should be in directory :  catdcd-4.0b/LINUXAMD64/bin/catdcd4.0/ Source the catdcd in your bashrc: export PATH="/path/to/catdcd/directory/:$PATH"
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Python : Turtle tree

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Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========
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USA COVID Tracking state-level COVID-19 case testing data

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