brainhack report template

LICENSE

@@ -1,22 +1,28 @@
-The MIT License (MIT)
+Copyright (c) 2014, Cameron Craddock
+All rights reserved.
 
-Copyright (c) 2015 Cameron Craddock
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+* Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 

Makefile

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+all: brainhack_report.tex brainhack_report.bib brainhack_report_maintext.tex
+	pdflatex brainhack_report.tex
+	bibtex brainhack_report
+	pdflatex brainhack_report.tex
+	pdflatex brainhack_report.tex
+#
+# marked: brainhack_report_v2_marked.tex brainhack_report.bib brainhack_report_maintext.tex
+# 	pdflatex brainhack_report_v2_marked.tex
+# 	bibtex brainhack_report_v2_marked
+# 	pdflatex brainhack_report_v2_marked.tex
+# 	pdflatex brainhack_report_v2_marked.tex
+
+pandoc: brainhack_report_template.tex brainhack_report.bib brainhack_report.md
+	pandoc -s -N --template brainhack_report_template.tex brainhack_report.md -o brainhack_report_formatted.tex
+
+formatted: pandoc
+	pdflatex brainhack_report_formatted.tex
+	bibtex brainhack_report_formatted
+	pdflatex brainhack_report_formatted.tex
+	pdflatex brainhack_report_formatted.tex

README.md

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+CraddockGigscience2014
+========================
+
+Craddock et. al., connectomes gigscience review paper.
+
+To compile this paper you will need pdflatex and bibtex installed. This can 
+easily be accomplished on a Mac by install mactex. If you have linux you will
+want to install from a repository using a package manager such as 'apt-get' 
+or 'yum'. If you have a PC, I am not sure how you install latex.
+
+If you have make installed you can compile the paper using:
+
+    make
+
+Otherwise you will need to run the commands:
+
+    pdflatex craddockGigascience2014.tex
+    bibtex craddockGigascience2014
+    pdflatex craddockGigascience2014.tex
+    pdflatex craddockGigascience2014.tex
+
+The multiple runs makes sure that all references are resolved. If you do not 
+change the bib file you will not need to rerun the bibtex command.
+
+Otherwise you can just download the PDF.
+