Ivan's essential bookmarks
Contact me at: ivangreg at yahoo co uk
Search engines
- Google - Advanced Search
- Google - Linux pages
- Google - Send text to phone
- Freeality Email Addresses and Reverse Lookup
- Cingular wireless Free2Go
Email_resources
- YahooMail
- Notre Dame Webmail
- Google Mail
- NIH Webmail
- Mail2Web
Career links
- Bioinformatics (the journal)
- Sciencemag Carrers
- Nature Jobs
- St. Jude Children's Research Hospital
- Opportunities for postdocs at the ASCB
- Some academic Bioinformatics and Computational Biology programs
Latex Resources
- Comprehensive TeX Archive Network
- The Indian TeX Users Group
- The LaTeX Font Catalogue
- Difference between latex and pdflatex
- Converting bitmaps to eps (for latex)
Programming
- Vim documentation
- Vim Reference guide
- Some of the most often used Vim commands
- C programming notes
- C course at The University of Nijmegen
- C course at The University of Strathclyde
- Programming in C (a reference website)
- The GNU C Library
- C++ resources at Linux Self Help
- Allocating vectors and arrays in C++
- Sample programs with multi-dimensional vectors in C++
- Bash Shell Programming in Linux
- Advanced Bash Shell Programming in Linux (Scroll down to get to the link. Awesome site.)
- Practical UNIX & Internet Security
- UNIX Shell Script Tutorials & Resources
- Differences between the different unix shells
- Perl: passing arguments from the command line (by Jon Allen).
Math
- Advanced engineering Mathematics
- Autoregressive (Integrated) Moving Average Models -AR(I)MA-
Scientific Artwork
- Imagemagick: usage by example
- Xmgrace: plotting bar graphs
- Gnuplot
- LabPlot
- Scilab
Arts (general)
- The Art Institute of Chicago Museum
- The Snite Museum of Art
- RadioBlue 100.7 FM
Cine
- KelloggInstitute
- NotreDame: Film screenings.
- ISSA Film Series
- Hollywood.com
Performing arts
- SouthBend Symphony Orchestra
- Notre Dame Concert Goers site
- Lyric Opera of Chicago
- Classical Live Online Radio Webcast - Classical Music.
Brain unrusters
- ZNet,Independent news and opinion publishers.
- LaNacion
- The Globe and Mail
- Le Monde diplomatique
- The New York Times
Fax
- HotCorp
- TPC.INT:Send a fax
MolecularBiology
- NCBI Home Page
- NCBI Bookshelf
- Sanger Institute
- Blastsearch
- Blast Mouse Traces
- Blast The Mouse Genome
- COILS Server
- Primer3 Input (primer3_www.cgi v 0.2)
- WebLogo
- A very nice way to display consensus in multiple alignments
- BAMBE at France
- Bayesian inference of phylogeny
- MrBayes at UK
- Bayesian inference of phylogeny using MCMC
- Phylip at France
- Felsenstein programs. (recommended)
- Phylip at Singapore
- Felsenstein programs
- Box Shade at Switzerland
- (recommended)
- Box Shade at France
- READSEQ Sequence Conversion Service
- Fix corrupt msf files
- Pedro's BioMolecular Research Tools - Part 1
Cell biology and histology
- Image and Video Library
- Allen Brain Atlas
Genomic scale projects
- GermOnline
- The Sanger Centre: Sequencing Projects
- Genome Net WWW server
Dictionaries, Encyclopoedias and Libraries
Journal Club assignment
- Nature
- EMBO
- Journal of Molecular Evolution
- Molecular and Cellular Biology
- EncyclopaediaBritannicaOnline
- xrefer
- Medicus Abbreviations
- Compendio de abreviaciones incluyendo nombres de journals.
- The World Electronic Text Library
- yourDictionary.com
- Kaplan Medical
Useful Linux commands
Is there any text file with 480 lines in this directory?
wc *.txt | grep 480
How many tif files I have in this directory? (imagine that you have 30000 tifs and ls can't handle that many arguments)
ls -l | grep '\.tif' | wc -l
Yeah... I did it with awk but I can't remember exactly how...
history | grep awk
Archiving (and moving) files
tar -cvf - *.txt --exclude unwantedfile.txt --remove-files | gzip -v9 > archive.tar.gz
What's the content of that archive?
unzip -v archive.zip
tar -tvf archive.tar
tar -tvzf archive.tar.gz
or in a longer fashion
gunzip < archive.tar.gz | tar -tvf -
Unpacking a specific file from the archive
gunzip < archive.tar.gz | tar -xvf - file.txt
unzip archive.zip -xv innerfile.txt
Creating a CD or DVD image from the content of a directory
mkisofs -r -J -o ./myimage.iso /mydirectory/
Creating a CD or DVD image from a CD or DVD (clonning)
dd if=/dev/cdrom of=myimage.iso bs=2048
DVD burning
dvdrecord -v -dao speed=4 dev=0,0,0 dvd.iso
Show every other line
awk '(NR%2==0) {print $0; }' input.txt
Calculate the average of the values in the first column of data
awk '{sum += $1}; END {print sum/NR}' input.txt
How many lines with the second and fourth columns equal to 5.3 I have in this matrix?
awk '($2==5.3 && $4==5.3) {print $0; }' matrix.txt | wc -l
How many lines in this matrix do not have 7 columns?
awk '(NF!=7) {print $0; }' matrix.txt | wc -l
Now a nice perl one-liner that works like awk. It prints the second and fifth column if the first column value is 'somestring'
cat mytable.txt | perl -lane 'print "@F[1,4]" if @F[0] eq 'somestring''
And since we are into perl one-liners, here is another one
echo 'censorship' | perl -wlane 'while (length($F[0]) > 0) {print $F[0]; chop $F[0];}'
Somebody stop me!! I can't stop writing one-liners!!
echo 'undone' | perl -wlane 'print @F; $F[0] =~ s/^un//; print @F'
Counting the number of elements per line
perl -wlane 'print $#F+1' mytable.txt
Counting the number of elements per line, skipping the first line
perl -wlane 'next if $. == 1; print $#F+1' mytable.txt
Checking printers and printer jobs
lpstat -a or lpq or lpc (...and then status -it may require superuser atributes)
Sending a printing job
lpr -P ChemOfficeColor3700 -o sides=two-sided-long-edge -o page-ranges=1-4,7,8 postscriptfile.ps
To cancel a printing job in a particular printer, first find the printing job number (say 12345) and then delete it as in this example
lpq -P ChemOfficeColor3700
lprm -P ChemOfficeColor3700 12345
Sorting a table first on the second column and then on the fisrt
sort -k 2,2 -k 1,1 table.txt
if the second column has to be ordered by numeric value use
sort -k 2n,2 -k 1,1 table.txt
if the numbers are in scientific notation it is better to use a less efficient but more robust option
sort -k 2g,2 -k 1,1 table.txt
The sort command can accept pipes with the dash, ie
awk '{print $0; }' table.txt | sort -k 2g,2 -k 1,1 -
Finding recursively all directories beginning with M:
find -type d -name 'M*'
Finding all pdfs recursivelly but excluding the EXCLUDEME directory
find -path './EXCLUDEME' -prune -o -name '*.pdf'
Finding a file by its content:
grep 'John Smith' *.txt
same thing but with color highlighting
grep --colour 'John Smith' *.txt
Recursive grep: find all .txt files containing the string John Smith. (Recursive grep can ONLY be done by combination of find and grep. For more info type info grep)
find . -name '*.txt' | xargs grep 'John Smith' /dev/null
If the output of find contains spaces, grep will not understand it. That can be fixed changing the spaces to "backslash spaces" globally
find . -name '*.txt' | sed 's/ /\\ /g' | xargs grep 'John Smith' /dev/null
Note: the line above is worth as an illustration of double piping but the robust way of passing arguments from find to xargs is this
find . -print0 -name '*.txt' | xargs -0 grep 'John Smith' /dev/null
A nice case would be the combination of these last cases, like this
find -path './YESTRDAY' -prune -o -name '*.txt' | sed 's/ /\\ /g' | xargs grep --colour 'John Smith' /dev/null
Checking partition space and AFS quota respectivelly
df -hk
fs lq ~
How much space are pdf files using in my current directory?
du --block-size=1K *.pdf | awk '{sum += $1}; END {print sum}'
find . -name '*.pdf' | xargs du -c
How is the volume of my data distributed among directories?
du --block-size=1K ~ | sort -k 1n,1 -
now the same thing including files, reporting in MBites and excluding the directory YESTRDAY,
du -a --block-size=1M --exclude=YESTRDAY ~ | sort -k 1n,1 -
and now a variation: listing recursivelly all pdf files ordered by size
find -path './YESTRDAY' -prune -o -name '*.pdf' -ls | awk '{print $7, $11; }' | sort -k 1n,1 -
Creating a 1000kB file
dd if=/dev/zero of=./testfile bs=1024 count=1000
Is LaTeX installed in this computer?
rpm -qa | grep latex
Is Firefox locked up? Then unlock it like this
rm -vf ~/.mozilla/firefox/*.default/.parentlock
Changing file atributes with chmod. There are three user levels, u(user), g(group) and o(other). There are three types of access: r, w and x. For instance, to block read access to the group
chmod g-r fileordirectory
and to grant executable access to the owner
chmod u+x fileordirectory
Important to note: attributes do not work the same straightforward way for directories and files. For directories, the x attribute grants access to it.
Breaking up a single line of xml code into one record per line. This is an example to clean a B3 database file
sed -e
's/<\/Book>/<\/Book>\n/g' -e
's/<\/Article>/<\/Article>\n/g' -e
's/<\/Misc>/<\/Misc>\n/g' dbin.xml > dbout.xml
Cleaning up the double bracket in the "Title" field in of the bitex export of B3
sed -e
's/^\tTitle = {{/\tTitle = { /' -e 's/}},$/ },/' dbin.bib > dbout.bib
vim and regular expressions. Grouping and backreferences. An example with search and replace. To match "good anyword" and make it "better anyword" in the current line, do
:s/good \(.\)/better \1/
Loops in awk, by example. Task: to write a list of numbers from 1 to 10. Solution with while: write to file.awk the following code
BEGIN {}
{}
END {
x = 1 # this line could instead be inserted in the BEGIN block
while (x <= 20) {
print x
x += 1
}
}
And now a solution with for:
BEGIN {}
{}
END {
for (x=1; x <= 20; x++) {
print x
}
}
and then run it as awk -f file.awk.
Changing image colors with convert. This example shows how to change the blue channel into the red channel.
convert input.gif \( +clone -channel B fx R \) +swap -channel R -fx v.B output.gif
Actually, what that has done is swap the Red and Blue channels. If you want to change a specific blue (say 0,0,239) into a specific red (say 255,0,0), this this is the way
convert input.gif -fill "rgb(255,0,0)" -opaque "rgb(0,0,239)" output.gif
and to modify the color of all the gif files in the current directory, we must use mogrity rather than convert
mogrify -fill "rgb(255,0,0)" -opaque "rgb(0,0,239)" *.gif
Note: use with caution. mogrify overwrites the original files.
Matlab
Running Matlab in command line mode
matlab -nosplash -nodesktop -nodisplay -nojvm
Running Matlab in non-interactive mode. Assuming that the code is in the file mycode.m, the syntax is
matlab -nosplash -nodesktop -nodisplay -nojvm -r mycode
Example of how to generate and save a figure in non-graphical environment. Launch Matlab in command line mode and type
X = [0:0.1:7];
figure; close
plot(X,sin(X));
print(gcf, '-depsc2', 'myfigure.eps');
Blah...