text:
MINC/Tutorials/SourceInstall

Installing MINC from sources, using cmake superbuild
Read installation instructions at https://github.com/BIC-MNI/minc-toolkit

Installing MINC from sources, using big makefile (outdated)
The MINC tools have been successfully compiled on a wide variety of systems. Including SGI, Sun, Linux, Windows, Mac OS X and VAX. This tutorial covers how to install the minc tools by compiling the sources. The tutorial presumes that you are using GNU/Linux, the procedure to build on other platforms is sometimes subtly different but will largely follow the example below.

Prerequisites
The MINC tools have a relatively large number of dependencies. The exact list of packages that needs to be installed before successfully compiling all the tools will depend on the target system, as every distribution of Linux/BSD comes with a different package set. In a new installation of Debian or Ubuntu, the following packages might be missing and need to be installed using apt-get or synaptic :

also, latex tools might be necessary to build the documentation. The following packages are required only if installing Display and/or register: This does not apply, however, for Nvidia-based video cards, which have their own libraries installed with the drivers. To check for these libraries, type:
 * HDF5
 * NetCDF
 * flex
 * g++ (older versions of N3 require g++ 4.2, yet there is no such restriction for the latest N3 release)
 * zlib1g-dev
 * libnetpbm9-dev
 * libxmu-dev
 * libxi-dev
 * libtext-format-perl
 * autoconf
 * byacc
 * opengl (libGL) dev
 * glut (libglut) dev

A window with rotating gears should appear.

To install everything in one go via apt-get on Ubuntu or Debian, this should suffice:

In order to build the packages you might also need to install the compiler and GNU make:

Building from the source code using one big makefile
A very large Makefile has been constructed, which builds much of the MNI-BIC content found on http://packages.bic.mni.mcgill.ca/tgz, in addition to a few other bits and pieces (notably parts of ITK). Please note that this process downloads, builds, and installs from source, and as such, if used, should be used instead of the aforementioned binary options (e.g. apt-getting minc-bundle). In addition, the presence of other minc libs from previous binary installs might result in the linker grabbing an older library, so it's best ensure that all previously installed minc components (e.g. netcdf, hdf5, etc) are removed prior to building. This method has been tested on several recent Linux distributions: Debian 5, Ubuntu 10.04, 10.10 & 11.04.

Step 1: Download the Make file
This file is currently part of Vlad Fonov's EZminc package, so that's where to find it. If problems, contact Vladimir Fonov .

Step 2: Decide on what you want to build
The Makefile provides quite a few build targets, the two extremes being make minc-only and make minc-full. Type make help to get a little help info, or take a look at the Makefile header with your favorite text editor in order to read details on all targets.

Step 3: Create your build and install directories
The Makefile downloads source packages and builds them in a user-defined build directory, specified via the BUILD_DIR argument. Create this directory prior to starting the build. If not specified, the build will occur in your current directory (which is messy). All build products will be installed to the specified INSTALL_DIR. Note that if you want to install to a system directory, say, /usr/local/bic, you will need to run the Makefile under sudo.

Step 4: Ensure that prerequisite packages are installed
Even though the big Makefile builds a lot of stuff, there are still some non-MNI-BIC packages that will need to be installed prior to the Make. Simply apt-get these packages; the Makefile header contains the apt-get statement that should do the job.

Step 5: Run your build(s)
OK, now for the moment of truth. Here are some build examples:

 * Minimal build: netcdf, hdf5, minc

 * Full build: Build lots of stuff, plus register and Display, and install the MNI-BIC fitting models

Please note that if anything goes wrong in one of the builds, the building of all dependent packages will not be attempted. To fix build errors, simply go into your BUILD_DIR/package_name directory and have a fiddle. As a matter of fact, this sort of fiddling is currently required when building Display under Ubuntu Lucid LTS (make visual), due to problems with libtool.

Building individual packages
It's possible to compile the MINC tools from individual packages. A typical installation will require:
 * minc-2
 * mni_autoreg
 * bicpl
 * conglomerate
 * ebtks
 * classify
 * inormalize
 * Register
 * mincblob
 * mincmorph
 * mni_perllib
 * N3
 * ray_trace
 * Display

Valuable additional scripts can be found here: http://packages.bic.mni.mcgill.ca/scripts/; these can be downloaded after the MINC tools have been installed.

First download the latest version of the MINC 2.x toolchain from http://packages.bic.mni.mcgill.ca/tgz

$ wget http://packages.bic.mni.mcgill.ca/tgz/minc-2.0.18.tar.gz

Then untar the package

$ tar zxvf minc-2.0.18.tar.gz

Enter the directory

$ cd minc-2.0.18

At this stage you should of course read the README file, and NEWS and ChangeLog files to discern what changes have been made since the last release. Lets presume you have done this.

In our case we want to install all the MINC Tools in /usr/local/bic and know that NetCDF and HDF5 have been previously installed in /usr/local. As such we will configure the package like this:

$ ./configure --with-build-path=/usr/local --prefix=/usr/local/bic

Note that with the minc2 libraries you will need to add an additional flag:

$ ./configure --with-minc2 --with-build-path=/usr/local --prefix=/usr/local/bic

A bunch of output will result from this command as configure checks for various libraries on your system. Running configure should generate a makefile. Which we can now use

$ make

This will build all the MINC files and now we can run the inbuilt checks that come with the MINC package. This is one of the advantages of building MINC from source as you can run the checks yourself, binary packages do not afford this possibility as the presumption is make that a build on one system will be fine on another system of the same platform. To run the checks type:

$ make check

The checks that are running will determine if underlying MINC API is self consistent plus a few other checks. Once the checks are complete the status is returned. You should see a line similar to this:

All 3 tests passed

It is now time to install MINC, given that we provided configure with a prefix argument this is the directory where the MINC API and base tools will be installed. In our case this is /usr/local/bic to do this type the following:

$ make install

This will install a number of things into four subdirectories in /usr/local/bic. Executable programs in bin/ header files in include/ library files in lib/ and manual pages in man/.

We can test the installation with something like this:

$ mincmath -version

This should return both the version number of the program and the underlying libraries.

title: MINC/Tutorials/SourceInstall


text:
MINC/Tutorials/BinaryInstalls

MINC has pre-built binaries for the following distributions/architectures

Debian GNU/Linux || Ubuntu
For this build type the dpkg and apt-get style of installation is used. The source deb files can be found here

http://packages.bic.mni.mcgill.ca/debian-lenny

For a different system, deb needs to be replaced by the appropriate extension (for example ubuntu-maverick). See Installation for a list of supported operating systems. To install the packages do this:

NB: when using Ubuntu use sudo to run the following commands (ie: add a "sudo" to the front of all of the following steps. If not, run the following commands as root.

Step 1: Run the following to add a line to /etc/apt/sources.list to tell apt-get to look at the packages website for the MINC packages.

# echo "deb http://packages.bic.mni.mcgill.ca/debian-lenny ./" >> /etc/apt/sources.list

Alternatively, using the graphical interface, go in "System>Administration>Synaptic manager>Configuration>Settings" and click on add. Then add the line "deb http://packages.bic.mni.mcgill.ca/deb ./" and click on "add source". For some reason, this will generate two new entries in the list of repositories. Click on the "MINC (sources)" repository and click "remove" to avoid getting error messages latter on.

Step 2: Update the internal list of packages

# apt-get update

Alternatively, using the graphical interface, click on "update" in synaptic manager.

Step 3: Install you packages of choice (here we install MINC, mni-autoreg and all the mni-models packages).

# apt-get install minc mni-autoreg mni-models*

Note that, when available, the minc-bundle package will install all minc tools & associated softwares. Alternatively, using the graphical interface, search for the package in synaptic manager, right click on the package name, select "install" and then click on "apply changes". A tutorial on synaptic manager can be found on help center".

Mac OSX Jaguar/Panther/Tiger (10.1-10.4)
For this build type the NeXT .pkg style of installation is used (given that this is what Apple use for OSX). The source packages can be found here

http://packages.bic.mni.mcgill.ca/osx

To install the packages do this:

This should apply to both an Intel and PPC Mac but when I wrote this I was fiddling with a MacBook

Step 1: install X11 and XCode from the Install DVD that came with your mac. X11 is part of the Optional Packages on you installation DVD, you will find it as X11SDK.pkg in the Tools/Packages subdirectory on the Xcode DVD (generally!)

Step 2: download the packages you want from the site above

Step 3: Click on each of the packages in turn and then press OK/Agree a lot of times for each one.

Step 4: Realise that step #3 is somewhat tedious and use a Command line to do it. To do this, first untar the packages and then install using "installer"

$ tar zxvf minc-xxxx.pkg.tar.gz  $ sudo installer -target / -pkg minc-xxxx.pkg

Note that in Step #4 we use sudo so that the packages are installed in /usr/local/mni. Note also that the installer command can take multiple .pkg files at once so you could so something like this to first untar all the packages in the directory in which you downloaded them and then install them

$ for i in `ls -1 *.pkg.tar.gz`; do tar zxvf $i; done $ for i in `ls -1 *.pkg`; do sudo installer -target / -pkg $i; done

Now all you need do is ensure that you have an install of netcdf on your mac somewhere. If you dont know if you do, then you likely dont... The easiest way to get netcdf is via the fink project. First, install fink (www.finkproject.org) if you dont have it. It will be installed at /sw/bin/. Then type:

$ sudo fink install netcdf

to get netcdf. While you are at it with fink you may as well install netpbm that is required by register and Display:

$ sudo fink install netpbm

Then you should be done

XP/Cygwin
For this build type I have not yet figured out a nice consistent way to build .deb dpkg files under debian that work. Nor have I put the time into figuring our the cygwin installer package structure (but will eventually). So what this means is that the cygwin download is a static .tar.gz archive of pre-compiled binaries that I build and release from time to time.

http://packages.bic.mni.mcgill.ca/cygwin

To install the packages do this:

Step 1: Download Setup.exe from the Cygwin website and install Cygwin. I use the following settings:

Root Directory:    C:\cygwin    (All users/UNIX file type) Local Package Dir: C:\cygwin\dnld

Step 2: Add the packages in the X11 and development sections

Step 3: Download the latest static build of the MINC toolset from the webpage mentioned above. Move this file to C:\cygwin\usr\local

Step 4: Start a cygwin shell and then run the following to "install".

$ tar zxvf minc-xxxxxx.tar.gz

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: MINC/Tutorials/BinaryInstalls


text:
MINC/Tutorials/InstallingPerl

The base MINC package and a number of the extra packages use a few PERL modules that are not installed on many systems by default. The most common of these are mni_perllib and Getopt::Tabular. You can get mni_perllib from here:

http://packages.bic.mni.mcgill.ca/tgz/mni_perllib-xxxx.tar.gz

Other PERL modules can be downloaded from CPAN

http://www.cpan.org

Step 1: Download the packages you need

Step 2: untar them

$ tar zxvf mni_perllib-xxxx.tar.gz

Step 3: enter the directory

$ cd mni_perllib_xxxx

Step 4: use Perl to make the real Makefile

$ perl Makefile.PL

Step 5: build the package

$ make

Step 6: Install it

$ sudo make install

title: MINC/Tutorials/InstallingPerl


text:
MINC/Tutorials/AddingPaths

All we need to do now is to add the executables to your PATH environment variable. This is different depending on whether you use a sh or csh shell variant. In our case and for the remainder of this tutorial we will presume we are using the bash shell. To do this in bash add the following line to your .bashrc file.

export PATH=$PATH:/usr/local/bic/bin

Whilst we are at it we should also add the manual pages.

export MANPATH=$MANPATH:/usr/local/bic/man

If we plan to compile other libraries or executables against the base MINC package we can also add the following to make life easier:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/bic/lib

Depending how you compiled MINC, you may have to export the path to the MNI PERL libraries as well :

export PERL5LIB=$PERL5LIB:$HOME/minc/perl

If you are using the MINC2 version of the libraries, but want to use the MINC1 format, you will also have to add :

unset MINC_FORCE_V2

To change the default level of internal compression (minc2 formal only, 0 is no compression, 9 is maximal compression):

export MINC_COMPRESS=7

Now all we need do is re-source our .bashrc file.

$ . ~/.bashrc

title: MINC/Tutorials/AddingPaths


text:
MINC/Tutorials/Tutorials01

By the end of this tutorial you should be proficient in the usage of the basic MINC commands such as mincresample, mincreshape and mincmath.

Basic MINC commands
Everything you do in MINC is based upon the idealogogy of Unix, that is tackle large problems with a combination of smaller programs that can be combined in many different ways. Whilst this is not the easiest system to learn, you will find it to be extremely flexible if you persevere and take time to learn the various ways that each of the commands can be used.

One of the ways to do this is to exhaustively read the man pages of all of the commands.

$ man mincinfo

Of course I would not recommend this if you are just beginning to use MINC as at this stage you are probably better to learn by example. However as you become more proficient with the commands you will find this very useful, albeit time consuming. A quick summary of help for each of the base commands can also be obtained at the command line by using the -help flag.

$ mincinfo -help

This will provide a listing of all the options that a particular command will take with a brief summary of its uses. Further details can always be found in the man page.

Whilst MINC programs are built on the Unix philosophy there is one differentation that is caused by the use of netCDF as the underlying library, pipes are not supported. This means that you cannot join the output of a series of MINC commands together using pipes. Instead you must always output the results of each command to a file. As such most commands follow the following convention:

$ mincxxx [options]

In some cases a MINC command will take multiple input files and as such the command will look like this:

$ mincxxx [options]  [ [...]]

You can ascertain as to which of these two most common variations the command follows by using the -help option. The usage information is output at the end of the help.

$ mincmath -help

At this stage you may be wondering the significance of the [] and <> brackets, this notation is commonly used to describe command line programs input. A [] bracket indicates an optional argument and <> brackets indicate a required argument.

Common options
There are a number of options that are common across many of the commands. They are:

-clobber

This option applies to the output file and should be used if the output file already exsists and you wish to overwrite it. If you do not use this option and the output file already exsists an error message will be printed and the program will exit without doing anything.

-verbose and -quiet

These options either increase or decrease the amount of output a command will produce. They have not effect on the result of the command merely the amount of information that is echoed to the screen.

-double, -float, -int, -short, -byte

These options specify the precision with which you desire the output of the current command. MINC has been designed such that at any stage you should not have to concern yourself with the datatype and range that your data is using. Your data is defined as existing as a Real (any positive or negative number) and a mapping is done internally to the current datatype.

The above figure demonstrates how an Image with a real (use-visible) range of 0 to 2000 can be mapped into a signed byte data type. Of course during this conversion the data will be discretised to 256 points of precision. It is for this reason that the choice is given to the user to choose the output precision for each MINC command should they wish a greater precision of output at any stage. If no datatype is explicitly chosen the MINC tools will use the datatype of the first input file.

-signed, -unsigned

Specifes as to whether a signed or an unsigned integer type is to be used for storage of data. Note that in most cases unless the data is being prepared for a specific purpose the user should not have to specify these options as the MINC file will rescale a real image range to either an unsigned or signed type with no loss or gain in performance or accuracy. These two options have no effect when used in conjunction with either -double or -float.

-copy_header, -nocopy_header

All MINC files have an integrated header that can contain any amount of metadata that is associated with a file. These options specify if this metadata is to be copied to the output file. Generally the default here is to copy the header from the first input file to the output file. There are many cases however in which you would not want to do this, for example if you are making a composite image (average) from a series of input files. In this case you probably do not want the metadata information from the first file including the subjects name, date of birth and other details copied to your output file.

title: MINC/Tutorials/Tutorials01


text:
MINC/Tutorials/CVSandPackaging

This is a HOWTO for creating a BIC package and some guidelines to release it upon the world

Package naming rules
The first thing you need to decide is what you are going to call your package. In general the prefix "minc" is reserved for packages/programs that will work on any MINC file (mincmath, mincresample, etc), be it 3D, 10D or even 1D. If your program/package is more suited to working on volumes (3D) then the suggestion is to prefix it with "vol". Granted this rule has not always been followed in the past (minctracc, mincmorph) but we needn't let that drag us back.

Your package name should also not contain UPPER CASE letters or underscores "_" as this will cause problems later on when you come to build binary packages for some systems (debian linux for example). Numbers and the dash character "-" are allowed in package names. Again, this rule has not always been followed (mni_autoreg for example) and subsequent pain has ensued.

Examples of good names include:

mincshazam - the name we shall use in the examples on this page volpls-fmri - a package to analyse fmri data via PLS mincinvert - a package/program to invert a file voldegibbs - a package to remove gibbs ringing from an image

Don't do this:

mincprocess - far too general vol-do-emma-processing - processing for emma, to generic and emma will leave eventually vol-do-something-with-a-really-long-name mincfoo mincb

Setting up CVS the BIC way
By now you have probably written some of your code and have it stored in your home directory, this is good as it is backed up but if you wanted to know what changes you made 3 days ago you will need something like CVS to track changes. CVS allows you to do this via repositories of code. This HOWTO will assume that from now on you are using CVS for your code and know how to use it. If not, you'd be best advised to go away and read this:

The current CVSROOT for the BIC is on cvs.bic.mni.mcgill.ca in /private-cvsroot so the following lines in your .bashrc will work wonders:

$ export CVSROOT=cvs.bic.mni.mcgill.ca:/private-cvsroot $ export CVS_RSH=ssh

In your case the second line is probably not needed as you will be local to the bic, but should you wish to use a remote repository then it comes in very handy.

You may also like to define a few defaults for CVS commands via a ~/.cshrc file, here is what I use and recommend

$ cat ~/.cvsrc checkout -P update -d -P diff -u -b -B tag -c # if you'd like cvs to be a bit quieter, comment out this # cvs -q

Use man to find out what these do but they are a good set of defaults for new users of CVS

Creating a package from scratch
Whilst it might seem like a large amount of overhead we use automake and autoconf to package source so that we can be sure that they will compile on a multitude of platforms. To get started with this, create yourself a local cvs directory

$ mkdir ~/cvs $ cd ~/cvs

Then export a copy of the BIC example package

$ cvs export -r HEAD libraries/mni-example-package

Then decide where you are going to place your package in cvs (take a look about /software/source).; If you need help with where to place your package send Andrew Janke an email: a.janke@gmail.com For now we'll assume that we are going to place our package in libraries. Rename the example package

$ mv libraries/mni-example-package libraries/mincshazam $ cd libraries/mincshazam

Place the name and email address of the package creators in the AUTHORS file

$ cat AUTHORS Andrew Janke

Add the licence you are going to use to the file COPYING. In this case we have used the MINC modified BSD style license. For guidelines/suggestions on which licence to use see Licensing below.

$ cat COPYING Copyright 2006-2007 Andrew L Janke McConnell Brain Imaging Centre Montreal Neurological Institute McGill University Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The author and McGill University make no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty.

Write the README. The README that you will already have in the current directory should be read and digested. It describes in better detail than this HOWTO where you can get more info on automake, autoconf and related tools. Remember that the README is the first file that a package builder will (or at least should) read.

$ cat README The mincshazam package contains mincshazam It does magic on minc files so amazing that all people should have it. If you don't like it, too bad.

Copy in your source file(s) and remove the examples.

$ cp ~/src/good_stuff/mincshazam.c. $ rm -f example_tags.c example_volume_io.c example_modify.c

Edit configure.ac to suit (read the autoconf man pages and the likes for more info). Suffice to say just editing the example that is given will suit most purposes. The most important parts to fill in are the three components of AC_INIT. Later when we build a proper BIC package this is the information that will be returned via the -version flag to your program.

$ cat configure.ac   # Require autoconf 2.57 or newer. AC_PREREQ([2.57]) # The arguments are package name, and package version. AC_INIT([mincshazam],[1.0], [Andrew Janke ]) # The argument is any source file distributed with the package. AC_CONFIG_SRCDIR([mincshazam.c]) AM_INIT_AUTOMAKE # The argument is the name of the generated header file. # It is recommended to leave it as "config.h". AC_CONFIG_HEADERS([config.h]) # This macro eases building the package; see m4/README. smr_WITH_BUILD_PATH # Checks for programs. AC_PROG_CC AC_PROG_INSTALL # Checks for libraries. See m4/README. mni_REQUIRE_VOLUMEIO # Finish up by writing output files. AC_CONFIG_FILES([Makefile]) AC_OUTPUT

Add your source files to Makefile.am. Again see the automake documentation for more info on this file. As always with anything to do with Make, be sure to uses tabs and not spaces when indenting. I suspect automake may handle spaces in some releases but you never know, best to err on the side of caution.

$ cat Makefile.am   AUTOMAKE_OPTIONS = check-news ACLOCAL_AMFLAGS = -I m4  bin_PROGRAMS = mincshazam EXTRA_DIST = $(m4_files) m4_files = m4/mni_REQUIRE_LIB.m4 m4/mni_REQUIRE_MNILIBS.m4      \ m4/mni_REQUIRE_OPENINVENTOR.m4                          \ m4/mni_cxx_have_koenig_lookup.m4 m4/smr_CGAL_MAKEFILE.m4 \ m4/smr_OPTIONAL_LIB.m4 m4/smr_REQUIRED_LIB.m4           \ m4/smr_WITH_BUILD_PATH.m4  mincshazam_SOURCES = mincshazam.c

Write your entry in the Changelog. The purpose of the ChangeLog is to communicate in simple(r) terms a summary of changes that you have made to a repository as part of a CVS commit to other developers. It need not be as detailed as the information you enter as part of the cvs commit but should instead contain a summary of the general reason for the changes.

$ cat ChangeLog 2006-04-06 Andrew L. Janke   * made this marvelous package * Added the -version option

Make an empty NEWS file. This file will get its turn when we make our first release later on.

echo > NEWS

You shouldn't have to modify anything in autogen.sh but we'll cat it here so that it doesn't feel left out. It probably already feels less important that configure.ac and Makefile.am for one good reason, it is. A script called autogen.sh is not required, you could just run the three commands listed below in order and all would be good. autogen.sh is merely a convention that most people who use automake and autoconf follow.

$ cat autogen.sh   #! /bin/sh set -e aclocal -I m4  autoheader automake --add-missing --copy autoreconf

Read README.CVS, remember it then remove it, the instructions it contains will be used later.

$ rm -f README.CVS

It is now high time we did our initial cvs import

$ cvs import -m 'initial import' libraries/mincshazam mni initial-import

The "mni" argument is the vendor branch and the "initial-import" argument is the tag that is associated with this operation so that you can return to the initial import should you wish.

Now remembering what you were instructed to do in README.CVS, do this:

$ cvs -d cvs.bic.mni.mcgill.ca:/private-cvsroot checkout -d m4 libraries/mni-acmacros

This will get you a copy of the most recent BIC m4 macros that are most commonly used. You should now have a directory called m4, it contains macros that autoconf uses to create the configure file for your package.

We are now finished creating our initial package, here is what you should have except of course with your own source files in there.

$ ls -F AUTHORS ChangeLog    NEWS    autogen.sh*   m4/ COPYING Makefile.am  README  configure.ac  mincshazam.c

Note that we get a copy of the m4 macros after our initial import such that we do not add them to our repository. We merely use them as a repository in its own right within our repository. Changes you make within m4 will be committed to the m4 repository. (be carefull here, others may well not like you much if you mess with the default m4 macros).

Building your package from scratch
At this stage you have files that automake and autoconf can process to form a configure script and then a subsequent Makefile. The first stage is to generate a configure script that you can distribute. Others who download a source version of your package will use this configure script to make a Makefile and then compile from there. The commands required to make configure script from the files you have are in the little shell autogen.sh

$ cat autogen.sh   #! /bin/sh set -e aclocal -I m4  autoheader automake --add-missing --copy autoreconf

Run autogen.sh

$ ./autogen.sh   /usr/share/aclocal/gtk.m4:7: warning: underquoted definition of AM_PATH_GTK run info '(automake)Extending aclocal' or see http://sources.redhat.com/automake/automake.html#Extending-aclocal /usr/share/aclocal/glib.m4:8: warning: underquoted definition of AM_PATH_GLIB configure.ac: installing `./install-sh' configure.ac: installing `./missing' Makefile.am: installing `./INSTALL' Makefile.am: installing `./depcomp'

The warnings above can be (very) safely ignored.

This will produce you a configure script, run it with appropriate options (./configure --help for more info). In our case we building against extra libraries that can be found in /usr/local/bic and also going to be installing our package in /usr/local/bic.

$ configure --with-build-path=/usr/local/bic --prefix=/usr/local/bic checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes <...>  config.status: creating Makefile config.status: creating config.h  config.status: executing depfiles commands

Presuming all went well with the configure step above, make your package. If things fail or you fail to get a Makefile the first thing to check is that you have up to date versions of automake and autoconf. Beyond this it really gets beyond the scope of this HOWTO.

$ make <...>

At this stage you should have a directory looking something like this:

$ ls  AUTHORS    Makefile.am  autogen.sh*      config.status*  m4/           stamp-h1 COPYING   Makefile.in  autom4te.cache/  configure*      mincshazam* ChangeLog NEWS         config.h         configure.ac    mincshazam.c   INSTALL    README       config.h.in      depcomp*        mincshazam.o   Makefile   aclocal.m4   config.log       install-sh*     missing*

Note that we do not need to add any of these automake/autoconf generated files to our cvs repository as they all can (and should) be regenerated for differing software platforms and versions of autotools.

Release procedure -- creating a source package to distribute
First decide on the type of versioning you are going to use for your package, typically only a dotted duple is needed. ie: 1.02 with occasional forrays into a dotted tuple if the package has many incremental releases (1.2.03).

Once you have a version numbering scheme in place, follow these set of rules (in strict order!)

1. If this is your first release, insert your initial version into configure.ac. If not, make sure that the version number is correct for this release. In our case, 1.0 is the first release so we can leave it as is from the previous section.

AC_INIT([mincshazam],[1.0], [Andrew Janke ])

2. update NEWS with info on the current release that can be digested by users of the package.

$ cat NEWS New in release 1.0 --  * Initial version.

3. Configure, build, and do a test install.

$ ./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni $ make $ make install

4. commit to make sure we are up to date in case someone else has made some changes to the package.

$ cvs commit

5. Create the distribution with distcheck.

$ make distcheck

This will make a file called mincshazam-1.0.tar.gz

6. Test build from this tarball on another system.

7. Copy the tarball to your distribution site. (in our case typically http://packages.bic.mni.mcgill.ca/tgz for source packages.

8. Tag your release so that you can return to this version anytime you want. The tag should follow the following format

-

In our case this translates to

$ cvs tag mincshazam-1-0

9. Update the version number in configure.in so that there is no chance that someone else or yourself can make a different release with the same version number. In this case it is best to update the version number only in the least most significant field.

AC_INIT([mincshazam],[1.1], [Andrew Janke ])

10. Commit the bumped version number

$ cvs commit.

adding binary building capability to your package
I really should finish this section

epm-header.in

adding a -version flag to your packages executables and scripts
blankety blank blank

Licensing types
Use the MINC one if possible (a modification of the older BSD license) or the GPL if you have included GPL code from elsewhere. A MINC tool that uses the GNU Scientific Library (GSL) is a good example of this.

other types in here?

migrating your cvs directory
The original home (for many years) of CVS at the BIC was shadow:/software/source. This changed on the 23/08/2006 such that we could finally have a public CVS repository and a split public and private portion of CVS.

If you have an existing cvs directory that is already checked out and would like to migrate it as you have some changes in it to the new server (cvs.bic.mni.mcgill.ca) then all you need do is edit the CVS/Root files in each respository that you have checked out to reflect the new home. The files should have a single line in them as such:

cvs.bic.mni.mcgill.ca:/private-cvs

I realise that this may cause some short-term pain but I do believe it to be for the better or I wouldn't have done it!

Good luck and email me (Andrew Janke - a.janke@gmail.com) if you have problems.

title: MINC/Tutorials/CVSandPackaging


text:
User talk:JOHNNY HEPHAESTOS~enwikibooks

This user talk page has been protected from editing to prevent JOHNNY HEPHAESTOS from introducing vandalism to it, posting abuse and nonsense or using the template after the denial of a previous request--Az1568(Talk) 18:29, 1 April 2007 (UTC)

Your account will be renamed
Hello,

The developer team at Wikimedia is making some changes to how accounts work, as part of our on-going efforts to provide new and better tools for our users like cross-wiki notifications. These changes will mean you have the same account name everywhere. This will let us give you new features that will help you edit and discuss better, and allow more flexible user permissions for tools. One of the side-effects of this is that user accounts will now have to be unique across all 900 Wikimedia wikis. See the announcement for more information.

Unfortunately, your account clashes with another account also called JOHNNY HEPHAESTOS. To make sure that both of you can use all Wikimedia projects in future, we have reserved the name JOHNNY HEPHAESTOS~enwikibooks that only you will have. If you like it, you don't have to do anything. If you do not like it, you can pick out a different name.

Your account will still work as before, and you will be credited for all your edits made so far, but you will have to use the new account name when you log in.

Sorry for the inconvenience.

Yours, Keegan Peterzell Community Liaison, Wikimedia Foundation 23:19, 17 March 2015 (UTC)

Renamed
 This account has been renamed as part of single-user login finalisation. If you own this account you can |log in using your previous username and password for more information. If you do not like this account's new name, you can choose your own using this form after logging in: . -- Keegan (WMF) (talk) 05:03, 19 April 2015 (UTC)

title: User talk:JOHNNY HEPHAESTOS~enwikibooks


text:
Cookbook:Equipment

Various types of equipment are used in a kitchen. One of the Wikibooks Cookbook's goals is to have an article on each, including uses, alternative equipment if you don't have the exact item, and a buying guide.

Hand tools
Kitchen hand tools are small, hand held tools that aid in cutting, slicing, stirring, combining, moving and serving. They usually have no or very few moving parts. Hand tools should be selected for sturdiness, durability and safety. The list of hand tools used in the kitchen is seemingly endless. Stick to the what you need for the kind of cooking you do. Add new ones carefully to avoid a drawer full of tools you don't need. "Time saving gadgets" are usually single purpose tools whose cost far exceeds their usefulness. For example, a mandolin is very useful if you slice a lot of vegetable frequently or you have a need for uniform slices for appearance, however, the time getting it out, setting it up and cleaning after use is not time very well spent if you are making a single salad.

Equipment index
For a complete, alphabetical list of equipment in the cookbook, visit Category:Cookbook equipment, or browse the subcategories below:

Adding equipment
To create a new equipment page yourself, enter your title directly behind the Cookbook prefix below.

ספר מתכונים/ציוד

title: Cookbook:Equipment


text:
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title: MediaWiki:Bad image list


text:
User talk:Orange~enwikibooks

Dag Orange, Mooi hoor zo'n Kaaps-Hollands gebouw, maar is dit nu echt toepasselijk voor een module over de Nederlandse taal? Worden die Afrikaners dan niet weer boos op ons. (Doen ze nog al gauw weet je..) Iarlagab 19:31, 1 April 2007 (UTC)

Ja zat er ook aan te denken, ik denk we kunnen een apart maar volwaaridg en uitgebreid hoofdstuk maken voor Afrikaans binnen de cursus.

Your account will be renamed
Hello,

The developer team at Wikimedia is making some changes to how accounts work, as part of our on-going efforts to provide new and better tools for our users like cross-wiki notifications. These changes will mean you have the same account name everywhere. This will let us give you new features that will help you edit and discuss better, and allow more flexible user permissions for tools. One of the side-effects of this is that user accounts will now have to be unique across all 900 Wikimedia wikis. See the announcement for more information.

Unfortunately, your account clashes with another account also called Orange. To make sure that both of you can use all Wikimedia projects in future, we have reserved the name Orange~enwikibooks that only you will have. If you like it, you don't have to do anything. If you do not like it, you can pick out a different name.

Your account will still work as before, and you will be credited for all your edits made so far, but you will have to use the new account name when you log in.

Sorry for the inconvenience.

Yours, Keegan Peterzell Community Liaison, Wikimedia Foundation 23:35, 17 March 2015 (UTC)

Renamed
 This account has been renamed as part of single-user login finalisation. If you own this account you can |log in using your previous username and password for more information. If you do not like this account's new name, you can choose your own using this form after logging in: . -- Keegan (WMF) (talk) 05:19, 19 April 2015 (UTC)

title: User talk:Orange~enwikibooks


text:
User talk:Iarlagab~enwikibooks

Welcome bij Wikibooks. Ik ben ook bezig op de Franstalige Wikibooks. fr:Néerlandais en fr:Néerlandais dans le secondaire--Oualmakran Youssef 19:34, 1 April 2007 (UTC)

Food
Goedenavond. Dutch/Vocabulary/Food is heel mooi. Is deze pagina bedoelt voor beginners? Maar ik wist het woord meelspijs niet. Misschien kunnen we dit woord veranderen met pasta of zo?--Oualmakran Youssef 18:38, 6 April 2007 (UTC)

Goeiemiddag Youssef

Meelspijs is een goed, zij het wat ouderwets Nederlands woord. Iarlagab 19:07, 6 April 2007 (UTC)

Hi from User:Zweifel
Hey -- I haven't logged into Wikibooks in a year. I got your message today. I am definitely going to check out your Dutch Wikibooks, because I've been casually learning Dutch for a while. Prepositional adverbs are awesome. Anyway, it's cool that there are grammar geeks out there. I'll catch you later.

BTW, I am User:Zweifel on Wikipedia. Zweifel (talk) 15:02, 14 February 2008 (UTC)

Iarlagab=Jcwf
When consolidating my user accounts I dropped the Iarlagab one. Please user Jcwf for any comments. Jcwf (discuss • contribs) 00:12, 16 August 2011 (UTC)

Your account will be renamed
Hello,

The developer team at Wikimedia is making some changes to how accounts work, as part of our on-going efforts to provide new and better tools for our users like cross-wiki notifications. These changes will mean you have the same account name everywhere. This will let us give you new features that will help you edit and discuss better, and allow more flexible user permissions for tools. One of the side-effects of this is that user accounts will now have to be unique across all 900 Wikimedia wikis. See the announcement for more information.

Unfortunately, your account clashes with another account also called Iarlagab. To make sure that both of you can use all Wikimedia projects in future, we have reserved the name Iarlagab~enwikibooks that only you will have. If you like it, you don't have to do anything. If you do not like it, you can pick out a different name.

Your account will still work as before, and you will be credited for all your edits made so far, but you will have to use the new account name when you log in.

Sorry for the inconvenience.

Yours, Keegan Peterzell Community Liaison, Wikimedia Foundation 23:13, 17 March 2015 (UTC)

Renamed
 This account has been renamed as part of single-user login finalisation. If you own this account you can |log in using your previous username and password for more information. If you do not like this account's new name, you can choose your own using this form after logging in: . -- Keegan (WMF) (talk) 05:03, 19 April 2015 (UTC)

title: User talk:Iarlagab~enwikibooks


text:
Talk:Lucid Dreaming/Introduction

Discussion "Misgivings about the book's approach" moved to Talk:Lucid Dreaming.

Does anyone else think that this is a little harsh when it talks about the mentally ill? It seems as though it clumps every mental disorder together and considers the brain unstable for anything. Is how lucid dreaming affects them proven, or is it just a guess by the authors? Or is this a general consensus among the lucid sleepers? --Emlnxrz 15:30, 18 June 2004 (UTC)

 * I myself have never heard of all this stuff. r3m0t (cont) (talk) 08:13, 19 Jun 2004 (UTC)

Are they "levels" of sleep or "stages". Or aren't these actually used synonymously? --Spikey 04:53, 31 Jan 2004 (UTC)

 * Synonymous. I will change all uses to levels because they are usually called levels 1 to 4. r3m0t (cont) (talk) 05:02, 31 Jan 2004 (UTC)

 * Oh, and welcome to the lucid dreaming wikibook! Got any feedback? How's your dream recall going or have you not done anything? :) r3m0t (cont) (talk) 13:22, 2 Feb 2004 (UTC)

 * I haven't really tried any of this yet. I'll probably start working on my dream recall this summer or next schoolyear.  I'll be heading off to college, and it seems like a good time to start new things like a dream journal.  --Spikey 04:06, 3 Feb 2004 (UTC)

 * Cool. Any feedback, please tell me. And by the way, if you become LD obsessed, the ld4all.com forums is a good visit, despite the spiritual stuff floating around in masses. r3m0t (cont) (talk) 08:24, 3 Feb 2004 (UTC)

"We awake quite often throughout the night, but if it is for less than 3 minutes it is usually forgotten by the time we wake up."
 * Really?

 * source. Now that I look at it, it seems it only happens after some REM and not after every REM. I'll try to clarify... it's only quasi-awake (or pseudo-awake ;) ) anyway, you get hypnagogic/hypnapompic imagery which probably goes along the same lines as the dream.

 * Why can't I seem to remember hypnagogic/hypnapompic imagery?

 * I have found that it slips away as I get out of bed in the morning. Can't you remember that you have wierd thoughts, illogical, irrational etc. when you are still drowsy in bed? That is hypnagogic/hypnapompic imagery. Also voices and any other vivid odd feelings (such as falling). r3m0t (cont) (talk) 12:27, 25 Feb 2004 (UTC)

The "I can't control my dreams" section is badly written in my opinion. I can't do it better myself, so I just complain here instead. It's not clear if it refers to lucid dreams or not (this is an introduction, most people probably haven't much lucid dream experience yet). Further, I would say there are many levels of lucidity. You might vaguely know that you are dreaming without being able to control the dream, especially in the beginning. Control is something you practice. Moreover, the connection between the Mother Theresa section is quite week. What is it really about?

 * I'm glad you realise that you're able to correct it :). I was not referring to lucid dreams, but more the feeling of "watching" a dream and not "acting" in it. There certainly are different levels of lucidity, and lucidity in lucid dreams should generally increase with practice. Now that I look at the second paragraph of that question, I have no clue why I put that in. I'll take it out soon if I don't remember, or link it in more fully if I do. r3m0t (cont) (talk) 14:43, 7 Apr 2004 (UTC)

I believe the whole introduction feels more like a "Lucid dreaming FAQ". It answer questions newbie lucid dreamers might have rather than introducing the reader to the subject.

 * It seems to me to get the content through. r3m0t (cont) (talk) 14:43, 7 Apr 2004 (UTC)

Dissociation
What do you think about the addition I made to the Dissociation section (things you should NOT be experiencing)? It does seem a bit scary to me, is it worth including at all?

KC 23:08, 17 Apr 2004 (UTC)

Yes, it does seem a bit scary -- just about everything in that list has happened to me at one time or another in real life. "Finding oneself in a place but unaware of how one got there" ? I thought this happened to just about everyone the first few times they wake up in an unfamiliar place. I remember that happened when I woke up after the first time I spent the night at Grandmom's house.

Perhaps we should move the Dissociation section to a completely different page and merely link to it. Would dissociation be appropriate ?

-- anonymous

Hello from a wikinewbie! I have had many LD's and would like to offer a few comments, I have chosen to put them all here until I have more time, and hopefully sources other than my (and friends') experiences. Also please inform if I am breaking with convention in this post.

RE: "signs you weren't"...Entering a dream within a dream is a technique for better lucidity, also some of the most profound are when one already lucid enters another realm, often experienced as going to sleep when you already know you are dreaming. (one ref. would be works by Dr. Alberto Villoldo)

RE: Dissociation: I think it is scary, and maybe misleading. I think it's a great idea to have some mention here, but perhaps it could be shortened and refer to some authority on dissociative behavior. (If community thinks it's important enough to mention, then it's too important for us nonpsychology experts to advise much)
 * also on this topic, I feel that some of these things are common (if very brief), and may be a sign of personal progress. e.g. ability to see oneself as other can be healthy analization. I hate to over discourage folks on a good path, so while I'm not able to do better with this page, it strikes me as analogous to quitting playing an instrument if you suddenly play a song very well, or improvise music that is better than you thought yourself capable of.

I would appreciate knowing if I should post differently. Would it be helpful to this book to find links to forums, or maybe start a "recomended reading list" GreenTwin 18:36, 15 Oct 2004 (UTC)

 * Hello to you! There is no convention you should follow in the talk pages. If you'de like to contribute to the main book though, check Talk:Lucid Dreaming first for a few basic guidelines.

 * Dreams within dreams: I've never heard of that and can't think why it would work (beyond the placebo effect). Besides, that's a different case. That's somebody who knows about lucid dreams who then becomes lucid and uses that technique in order to gain better lucidity. The fact is, generally people who enter a lucid dream from within a dream aren't really lucid, they're only dreaming that they are.

 * Community no more. I don't have an opinion on the dissociation section because I don't understand it.

 * (Why did you indent that twice?) What do you mean by "ability to see oneself as other"? What do you mean by things being brief? What is "healthy analization"? Sorry, I don't understand you.

 * There is already a "recommended reading list". It's called "Further Reading" and it's on the nav:

 * It includes links to forums and books. r3m0t (cont) (talk) 07:52, 17 Oct 2004 (UTC)

I'm a little concerned that the book presents 'symptoms' that only a few may have experienced as concrete aspects of Lucid Dreaming. Most of the list of dissociations could possibly be explained by other psychological explanations and not related to Lucid Dreaming, and yet here they are being listed as factual symptoms.

It might be better to have this introduced as things that some people have experienced whilst attempted to experience Lucid Dreaming'.

- Matt 18:15, 15 April 2005 (GMT)

Spinning?
"Attempting to spin" - what does it mean? If it means literally spin, what is so special about it? And if you use a different meaning, please elaborate.

 * Anything that gives your senses input from the dream world is fine. Spinning is a good way to "lock" yourself more into the dream consciousness, by asking your brain to generate more substance to the dream. Another way is to focus on dream visuals to make them more stable. Am I making any sense? KC 22:03, 18 May 2004 (UTC)

 * Yes, it means literally spin. It's the sort of thing which somebody who knows about lucid dreaming would do. It's the sort of thing I do in a lucid dream, because it prolongs my dreams (see LD Using and the above post) r3m0t (cont) (talk) 06:21, 19 May 2004 (UTC)

Reasons to pursue lucid dreaming
Thanks for all the work you have put into this wikibook. When I came upon this subject initially, I had one central question on my mind. Namely, is lucid dreaming a fruitful pursuit, or merely a frivolous diversion from the transcendental purposes of life? I decided to give lucid dreaming a try. I got a notebook and began to record my dreams. I began to ponder the matter of how I knew during waking moments that I was in the physical world. I hydrated copiously before retiring. In the end I lost interest because I just couldn't convince myself there was transcendental purpose in lucid dreaming. It would be a great contribution to this Wikibook to have a more fully developed section about the rationale for studying/pursuing lucid dreaming. Does lucid dreaming enhance one's ability to understand and practice sacrificial love and to make the best use of one's time in this world? How? Why is it that the majority of discussion of lucid dreaming seems to be from a purposeless or frivolous perspective? I think all this would make a very interesting addition to the Wikibook. 216.160.223.49 21:41, 3 Jan 2005 (UTC)

 * Most people take it as a "frivolous pursuit". However:

 * Some people have said that meditating (or dreaming) within a dream has felt to them particularly deep, that they found it easier to relax, etc.
 * You can try shared dreaming from it as well as attempt astral projection.
 * Considering that (healthy people) spend about 1/3 of their time sleeping and 1/4 of their time dreaming, I would say that lucid dreaming aids effective use of time. You're using that remaining 1/12 of living life at not much cost to the rest of your time. As some people have reported solving problems in dreams, you might be able to solve some of your own. Also, your artistic side is probably more "open" - pasQuale dreamed up the two most recent designs of LD4all.com.
 * I would imagine that there is not much interest in lucid dreaming for spirituality because Stephen LaBerge, who proved lucid dreaming, did not publish any mention of it in his book. Therefore people went along the "fun and silly" route. However, I don't see why this should stop you from trying lucid dreaming, because it honestly is great fun and very satisfying when you become lucid. r3m0t (cont) (talk) 07:32, 5 Jan 2005 (UTC) PS You will get more replies by joining a forum or asking on alt.dreams.lucid. Check the "further reading" section.

last section and hypnosis
I believe the last part is way off. Self hypnosis as I understand doesn't lead to any visual/etc experiences and can't really be compared with lucid dreaming. Apart from the fact that you are interacting with your subconscious on a different level.

 * Well, it does say 'If you often enter a "dream world"' . . . but I see your point. I don't have any strong feelings about it either way; if you want to remove that part, go ahead. —Tharenthel (Talk) (Contribs) 23:07, 30 January 2006 (UTC)

False Awakenings
The section on false awakenings really needs improvement! I don't understand what it is about. Link it or expand it, something needs to be added. -- Phyzome 22:34, 8 March 2006 (UTC)

 * I tried to clarify it some. It does still need some work, but it hopefully makes more sense now. —Tharenthel (Talk) (Contribs) 06:19, 5 April 2006 (UTC)

Note
I've removed the reference to the "placebo effect".

The Note is really a Disclaimer. However this paragraph about the effect of your own expectations helps to avoid it just looking like a CYA move. Having said that, I think we want the Note to be nice and short.

The "placebo" reference is somewhat confusing. The paragraph is trying to make a wider point that theres a limit to how far any technique can take you; that in the end its your own attitude that determines how you dream. However the "placebo effect" refers specifically to a "pharmacologically inert" "preparation" - something that mimics medication, and is supposed to have no effect other than making someone think they're being given treatment, in a double blind trial or where there is no more effective alternative ("Headology", for the Prattchett fan).

The use of the phrase "placebo effect" could also be confused with the previous paragraph which is a disclaimer about the potentially lucid inducing substances listed later on in the book. TBH that's probably how the "placebo effect" paragraph originated, but I think my way is better :-).

Of course, since I'm editting this anonymously, haven't contributed significantly to this project etc., feel free to disagree violently and revert my change - but it'd be best if you could explain why I'm wrong.

Sourcejedi 20:12, 2 April 2007 (UTC)

Alienation
There was a rather good thread in Dreamviews where someone explained that people are likely to associate Lucid Dreaming with "New Age" spirituality (which it is to some extent, particularly in the AP community), and therefore dismiss it out of hand. Unfortunately the appalling search facility and sheer volume of posts has rendered it lost to me right now, but I think its worth trying to work in the idea somehow - just didn't manage to do it today!

Sourcejedi 20:12, 2 April 2007 (UTC)

Controversial:
This *needs* cleaning up. This is the first page in the book, and it doesn't look pretty.

Now the "evil spirits will take over your mind" section doesn't need the tag; yes its controversial, but its clear and explicitly mentioned in the content that this is a matter for your own belief. Labelling a matter of belief "controversial" is also in questionable taste - I don;t go around calling the belief that Jesus was the Son of God who died for our sins and rose again "controversial"; it is simply a matter of personal belief.

OTOH I can certainly see why the other sections were marked in this way - and why they weren't deleted out of hand. I'd suggest the way to treat this is as points in an argument about whether its safe to dream lucidly. I'm not saying the suggestions for help should go (e.g. the point about asking your doctor about meds if you think you've got a problem) - they're good too. I think most people will find their presence reassuring - that if they did have a problem, they would be able to find help, and its also good to show that we're serious and consider the possibility of harm - though as something which has not been proven.

Sourcejedi 20:12, 2 April 2007 (UTC)

*Mostly* Dead discussion
This whole book's discussion is pretty much dead, but if people have questions about Lucid Dreaming, drop a message at erik212's (me) talk page, or e-mail me at erikmuntean@yahoo.com. -erik212

title: Talk:Lucid Dreaming/Introduction


text:
Talk:Lucid Dreaming/Glossary

VD? Honestly? The expansion makes sense, but I've not seen that abbreviation and IMO I don't think people would use it to avoid reusing an abbreviation for an STD!

I wouldn't be so sure about putting new terms on this page, although it would be nice for this place to be a starter for it to catch on, and certainly your ideas (KM) are better than simply saying a reality check "failed" or "succeeded". Let's leave it for now. The Glossary isn't very important, anyway. r3m0t (cont) (talk) 21:18, 15 Apr 2004 (UTC)

title: Talk:Lucid Dreaming/Glossary


text:
User:Untrots~enwikibooks

Moooooooo!!!

title: User:Untrots~enwikibooks


text:
User talk:Untrots~enwikibooks

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Good luck!. Az1568(Talk) 20:54, 1 April 2007 (UTC)

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Wikijunior:Human Body/Introduction

Introduction
As humans, we have amazing bodies. Our bodies are made up of many parts that work together to keep us alive. These parts let us to do a lot of things: breathing, thinking, moving, tasting, touching, seeing, hearing, and some other things too, without which, our body can't work. Our bodies can do this because we give it food, water, and air, and these gives us energy, to make the body work. The point of this book is to help everyone who reads it, to learn about all about the human body: what it does, what it needs, what it's good at, and what it's bad at. With this book, you will learn all the basics about the human body. All of the contributors hope that you will learn a lot and have fun! Thank you for reading!

Let us start our exciting journey to discover our human body...

title: Wikijunior:Human Body/Introduction


text:
Advanced Interactive Media/Other Topics/Competition for Wikipedia

Of all the emerging technologies and advancements in communication, social networking paired with user created/contributed content is at an all-time high. We have websites like digg.com (one of my faves) that allows you to customize your profile to show you news related to what you are most interested in. Digg offers an easy online community for users to submit stories, photos, videos, etc.

Digg was founded by former TechTV host Kevin Rose and originally was more tech-geared. Digg has since seen an open market and expanded to allow users to submit news in other categories such as sports, entertainment, politics, etc. Digg's user base is still largely the tech community, so it's a great resource to keep up to date. Stories get voted on and promoted to the "front page". Once submitted, these stories can be commented on and "dugg", which is creating a social bookmark.

There are the obvious trendsetters in these communities such as Digg, Deli.cio.us, StumbleUpon, YouTube, MySpace, and Wikipedia just to name a few. Where are the competitors? In current news...a Wikipedia rival is set for release this week. Citizendium is the new guy on the block. Citizendium was created by Larry Sanger, many would call the co-founder of Wikipedia. What is so great about Citizendium? The questions that are raised by the online community are "Would Wikipedia be better if its contributors fully identified themselves? Would Wikipedia be better if it solicited guidance from academics and other specialists?" Citizendium takes a different approach in attempting to tackle these problems. Content can only be edited by approved editors who have credentials to prove their credibility. Editors/users must also use their real names when submitting and editing. According to sources, "Its volunteer-base numbers roughly 900 authors and 200 editors. The site has 1,100 articles, with 11 'approved' by editors."

For more info read the full article.

Wikipedia Competitor Seeks to Cut Out Errors


text:
Emergency Medicine/Arterial

Acute Arterial Occlusion
It happens when a embolus, most often from cardiac source, impacts in the arterial tree or when there is a local thrombosis, usually at the site of a atherosclerotic plaque or in patients with coagulation disturbance.

Signs and Symptoms
The main symptom is pain on the affected limb, it usually has a sudden onset, but may become worse with time. In patients with previously stenosis the first symptom may be only a worse or new onset of claudication.

The affected limb is also cold, pulseless e pallor. Peripheral nerves injury is usually an early manifestation, starting with numbness evolving to completely motor and sensitive deficit.

Patients who are seen very soon may complain of pain localized where the occlusion occurred, it may helps in the therapeutic approach.

Diagnosis
The diagnosis is usually made in clinical basis only. Image exams help to localize the site of obstruction, the extent of thrombosis and the source of embolus.

The main differential diagnosis are severe deep venous thrombosis (Phlegmasia) and compartimental syndrome.

Classification
Acute arterial occlusion is classified in clinical basis only.

Class I: Minor symptoms, limb is warm and no neurologic damage has occurred. Class II: Classic symptoms of acute limb ischemia, some neurologic damage, the limb must be viable. Class III: Complete neurologic damage, extensive skin necrosis. The limb is not viable.

Treatment
Except in cases where aortic dissection is a possibility, the initial treatment is anticoagulation. It helps to prevent clot propagation and lets internal fibrinolytic system acts.

Class I: No urgent treatment is necessary, the patient may be treated as a cladicant.

Class II: Urgent revascularization is necessary.

Class III: Amputation is the only treatment to be considered.

title: Emergency Medicine/Arterial


text:
Talk:Java Programming/History

More friendly history
I think that the history (especially the version history) should be more friendly and contain more historical and background information. And the actual features lists should be moved (after a good revision) to some kind of appendix. As it is now, new Java programmers, I think, can get confused by all those Java details. Untrots 22:08, 1 April 2007 (UTC)
 * The history is more flowing than before and information is more readily available. Information is cited. However, I'd have to do something about the version history. I think a simple table would be enough. And then all the version specifications can be kept in separate pages in an appendix. Arunreginald (talk) 09:48, 9 May 2008 (UTC)
 * The version history should be written like a story and not a list of groceries. Arunreginald (talk) 12:22, 10 May 2008 (UTC)

Heritage from Smalltalk
The significant influence of Smalltalk on Java is completely ignored in this section on the history of Java. Unless the reader explores the links to Wikipedia entries the reader may be left with the wrong impression that many of the key concepts of Java originated with the Java creators. The truth is that many of the concepts were already in use long before Java was created. Object oriented programming and the technology of the Virtual Machine had already achieved wider dissemination through, mainly, the Smalltalk object oriented programming environment.

What differentiates Java from Smalltalk is the disposal of the object model friendly syntax of Smalltalk in favour of a procedural C-like syntax and the replacement of the interactive interpreter oriented IDE for compilation based program development practice. These changes helped Jave to become the dominant Object Oriented software development tool because programmers found in Java much of what they were already familiar with: C-like syntax and compiled programs. The portability afforded by the Virtual Machine technology provided the bonus that made switching to Java worthwhile.

JoaquinS (discuss • contribs) 23:53, 3 December 2016 (UTC)

Java 8
When I came to this page, Java 8 was not included in the list of released Java versions. Java 8 was released way back in March 2014, making the history list very outdated, with Java 9 already being scheduled for release soon. As a side note, there is also an anachronism at the bottom of the same section, which states that "Java 8 will be released ... in summer 2013" (note the future tense as opposed to past tense). If someone would please update all of this outdated information, including all of the changes made in Java 8. 2602:302:D124:A0E0:C9E3:5557:BF4B:55F0 (discuss) 22:42, 29 June 2017 (UTC)
 * Done. Ftiercel (discuss • contribs) 17:23, 8 July 2017 (UTC)

title: Talk:Java Programming/History


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Good luck!

Xania talk 22:27, 1 April 2007 (UTC)

title: User talk:Aregueira


text:
User talk:72.226.193.192

Hi, I notice that your editing a lot of the Proteomics book. May I suggest that you create an account? Also, if you want an article from Wikipedia, please do not copy and paste it; instead, ask at WB:RFI. Regards, Iamunknown 22:40, 1 April 2007 (UTC)
 * Please consider signing up. Just click Special:Userlogin, click "Create an account" and fill out the few forms.  --Iamunknown 23:03, 1 April 2007 (UTC)

title: User talk:72.226.193.192


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Proteomics/Protein Separations- Electrophoresis/Types of Gel Electrophoresis/QPNC-PAGE

QPNC-PAGE

Quantitative Preparative Native Continuous PolyAcrylamide GelElectrophoresis is a technique to isolate active or native metalloproteins (e.g., metal chaperones, prions, metal transport proteins, amyloids, metalloenzymes, metallopeptides) in biological samples and to resolve properly and improperly folded metal cofactor-containing proteins in complex protein mixtures.

Gel Characteristics
The gel is polymerized for a time period of 69 hr at room temperature to fully-polymerize it. That results in a gel which is homogeneous, mechanically stable and free of monomers or radicals. Therefore, the interactions of the gel with the biomolecules can be neglected. The separated metalloproteins are not dissociated into apoproteins and metal cofactors. Highly purified metalloproteins can be isolated in quantitative amounts in a few specific PAGE fractions. The active structures or conformation of the isolated proteins do not change by using QPNC-PAGE.

Electrophoresis Buffer
The buffer used for electrophoresis contains 20 mM Tris-HCl, 1 mM NaN3 and has a pH 10. Due to the specific properties of the gel and buffer solution, most proteins in the sample are charged negatively and migrate from the cathode to the anode in the electric field. Although the pH value (pH 10.00) of the electrophoresis buffer does not correspond to a physiological pH within a cell or tissue, the proteins are eluted continuously by a physiological buffer solution (pH 8.00) and isolated in different fractions. The separation system including the electrophoresis chamber and a fraction collector is cooled in a refrigerator at 4°C.

Identification and Quantitation
Cd, Zn, Cu, Ni, Pd, Co, Fe, Mn, Pt, Cr, Mo and other metal cofactors can be identified and quantified by ICP-MS. Because of high purity and optimized concentration of the separated metalloproteins in specific PAGE fractions, the related structures of these analytes can be elucidated by using solution NMR spectroscopy under non-denaturing conditions.

Applications
QPNC-PAGE combined with biological mass and NMR spectrometries provide valuable information about the metabolisms of important metal cofactors in biological systems and the proper folding of metallochaperones in conformational diseases (e.g., Alzheimer's or related diseases). The quantitative analysis of metallochaperone proteins in biofluids (e.g., blood, cerebrospinal fluid) helps in the clinical investigations concerning the structure-function relationships of biologically-active metal cofactor-containing chaperones in those protein-misfolding diseases.


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Dutch/Practical

There are different words for newspaper in Dutch. In the Netherlands the word krant is used. In the Dutch provinces North-Brabant, Limburg and in Belgium Gazet or Gazette is used. Another word is Courant or in Afrikaans, the variant in South Africa and Namibia, written as Koerant. A Dagblad is a daily paper and a Weekblad comes once per week.

These examples of papers which are also online are very practical to learn reading Dutch.

[[Image:Flag of the Netherlands.svg|25px]] Nederlandse kranten, Dutch newspapers

 * http://www.telegraaf.nl - De Telegraaf
 * http://www.nrc.nl - NRC Handelsblad
 * http://www.volkskrant.nl - De Volkskrant
 * http://www.algemeendagblad.nl - Algemeen Dagblad
 * http://www.fd.nl - Het Finaciele Dagblad
 * http://www.parool.nl - Het Parool
 * http://www.trouw.nl - Trouw
 * http://www.nd.nl - Nederlands Dagblad
 * http://www.spitsnet.nl - Sp!ts
 * http://www.metronieuws.nl - Metro
 * http://www.refdag.nl - Reformatorisch Dagblad
 * http://www.nu.nl/

[[Image:Flag of Belgium.svg|20px]] Belgische kranten, Belgian newspapers

 * http://www.demorgen.be - De Morgen
 * http://www.standaard.be - De Standaard
 * http://www.gva.be - Gazet van Antwerpen
 * http://www.hbvl.be - Het Belang van Limburg
 * http://www.hln.be - Het Laatste Nieuws
 * http://www.nieuwsblad.be - Het Nieuwsblad

[[Image:Flag of Suriname.svg|25px]] Surinaamse kranten, Surinamese newspapers

 * http://www.dwtonline.com De Ware Tijd (DWT)
 * http://www.dbsuriname.com - Dagblad Suriname

[[Image:Flag of the Netherlands Antilles.svg|25px]] Kranten van de Nederlandse Antillen, newspapers of the Netherlands Antilles

 * http://www.antilliaansdagblad.com/ - Antillians Dagblad
 * http://www.antilliaansweekblad.com/ [dead link] - Antillians Weekblad
 * http://www.amigoe.com - Amigoe

[[Image:Flag of South Africa.svg|25px]] Suid-Afrikaanse koerante (Afrikaans), South African newspapers

 * http://www.dieburger.com/ - Die Burger
 * http://www.rapport.co.za - Rapport
 * http://www.dieson.co.za/[dead link January 2010] - Die son (mobile, working version)

[[Image:Flag of Namibia.svg|25px]] Namibiese koerante (Afrikaans), Namibian newspapers

 * http://www.republikein.com.na/ -Republikein

Zie ook, See also

 * http://www.kidon.com/media-link/nederlands.php - A collection of newspapers in Dutch, een verzameling van kranten in het Nederlands
 * enkele taalsites

title: Dutch/Practical


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Honda Nighthawk

Introduction
Welcome to the Honda Nighthawk owner repair and maintenance guide. The intention of this effort is to provide owners with helpful concise suggestions and procedures for working on specific Nighthawk models. It is not intended in any way to be used as a substitute for official Honda shop manuals. All procedures mentioned in this guide, where possible are cross referenced to specific pages and should be used in conjunction with the Honda manual.

Table of contents

 * /Guidelines for Contributors/
 * /Maintenance/
 * /Tire Selection/
 * /Carburetor Cleaning/
 * /Known Problems/
 * /Restoration/
 * /Long Term Storage/

Troubleshooting

 * /Starting/
 * /Suspension/
 * /Brakes/
 * /Fuel System/
 * /Ignition System/
 * /Handling/
 * /Lights/
 * /Charging/

title: Honda Nighthawk


text:
System Troubleshooting

Testing and troubleshooting a system can be a complicated process, and one that involves just as much standard methodology as design or manufacture. This book will discuss 10 steps to debugging and troubleshooting a system.

10 Steps

 * 1) /Don't Break It/!
 * 2) /Will touching this hurt me/?
 * 3) /Is it Broken to begin with/?
 * 4) /Don't cause any more problems/...
 * 5) /Establish a Start and End/
 * 6) /Sectionalize the System/
 * 7) /Verify Components/
 * 8) Finding the Cause
 * 9) Swapping out Components
 * 10) The Clean up!

title: System Troubleshooting


text:
User talk:83.131.194.18

Please stop adding nonsense to Wikibooks. It is considered vandalism. If you would like to experiment, use the sandbox. Thank you. Mattb112885 (talk) 01:19, 2 April 2007 (UTC)

title: User talk:83.131.194.18


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Talk:The Scientific Method

Hey WK, I really like this idea, I'd be willing to help you out with this one if you want (it'd be one of the few books you've started that I know anything about :)). Not sure how detailed you want to go, there's tons and tons of stuff out there on how to conduct a good experiment, but I'm not sure if that'd be part of your focus or if you just want to talk about what it is and what it isn't, and some history of famous experiments across the sciences. Mattb112885 (talk) 01:27, 2 April 2007 (UTC)

title: Talk:The Scientific Method


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Honda Nighthawk/Starting

 A General Guide to Trouble Shooting - Starting

contributed by author: doclockwood...700S rider/revivifyer)

HI, it looks like there's a lot of Nighthawk starting issues (on the list) right now. No doubt, it's mostly from all the winterized bikes coming out of hibernation and from plain old gettin' old, the bikes, I mean. If we have some common tips for starting woes, we could all post 'em to the same page and maybe save someone a little time and work by looking for help (t)here. Many many thanks to all who contribute.

Anyway, I have had my share of starting trouble lately, (I sure have a lot to learn about starters) but if there's one thing I'd check first, it would be:

1) Clean the grounds to frame and engine. Shine 'em up, coat 'em w/ something or other(not biting on THAT one...dielectric grease) and then follow up by cleaning all the contacts in the starting/charging circuit. Test 'em all with an Ω meter (couldn't "resist") and a manual. This includes the kill switch and starter button.

2) Make absolutely sure there's a fully charged battery. It may be necessary to buy a new one every season but that would indicate a charging issue. Even if it's just recently charged, it may lose it's cranking ability after just a few seconds when you hit the start button due to the age/inefficiencies of other components. Take a jump from a car and see if it's appreciably stronger(faster spinning starter) than the bike alone. Cleaner contacts and a "known" strong battery work wonders.

3) Install new plugs and wires. This makes an easier path for the battery juice...new plugs every oil change, even if the bike is running great? I dunno...to each his/her own. But it eliminates a variable if it won't start...new plugs can't hurt.

4) A rusty tank? Bad petcock? Got to be clean. And use fresh gas...my suspicion is that Sta-bil may inhibit restarting in the Spring for folx above the Mason-Dixon line...good stuff to keep the water out of the gas tank, but makes for hard starts initially. Another rookie mistake is to use Stabil in the tank but turn off the bike before it's had a chance to get all the way into the carbs and pistons...I'm certainly guilty of this one.

5) Carbs need to be clean, too. Just from the numerous posts on this topic, it's likely the carbs will gum up or clog sometime during your watch so it has to be considered a chronic problem for Nighthawks, esp. the older models. Lo-speed jets need attention here. Bad idle indicates clogged jets, but it may be electrical, too.

6) The starter should be in good condition. It seems like a no-brainer, but if all the above conditions are favorable, then a bad starter may be the problem. No duh, right?:) There are eBay starters out there and folk who refurbish them, so don't despair. 7) If the starter sounds good/performs well and the bike STILL doesn't start, it MAY be a bad coil, though it's a long shot. My bike was firing on cyls 2 and 4 only so I suspected the 1-4 coil as bad, but it was just a cruddy ground. A meter will confirm coil health.

Lots more tips are in the troubleshooting section in the NH 700S manuals in ignition/starting sections.

title: Honda Nighthawk/Starting