plot neural network in Latex

 

https://github.com/HarisIqbal88/PlotNeuralNet

latex thesis cover

 

The front cover can be edited in “ utthesis.cls” ( last one)  lines 200 - 231 .

draw a graph diagram on latex

 

https://www.baeldung.com/cs/latex-drawing-graphs

latexdiff

 

  latexdiff 

$  latexdiff    first_version.tex  second version .tex  >  marked_up_file.tex 

Latex submission to BMC

All Latex files and template should all be listed as Manuscript

bibtex, pdflatex

applejack:bmc_netwk_aging_manuscript hqin$ bibtex bmc_networkaging

This is BibTeX, Version 0.99d (TeX Live 2016)

The top-level auxiliary file: bmc_networkaging.aux

The style file: bmc-mathphys.bst

Database file #1: qin_networkaging.bib

pdflatex bmc_networkaging

pdflatex bmc_networkaging

bibtex citation style, BMC articles

For books, BMC articles require address or publisher. Other wise, it print three question marks, "???"

latex, multiple panel figure

More at:
https://tex.stackexchange.com/questions/271518/multiple-panel-figure-with-figures-side-by-side/271522

multiple panel figure in latex. The arrangement is partly controlled by "%", unbelievable.

\documentclass{article}
\usepackage{graphicx}
\usepackage{subcaption}

\begin{document}

\begin{figure}
\centering

\begin{subfigure}[t] {0.4\textwidth}
\centering
\includegraphics[width=\linewidth]{FiguresTables/pdf/BY4742.pdf}
  \caption{}
  \label{Figure:fig_a}
\end{subfigure}
%
\begin{subfigure}[t] {0.4\textwidth}
\centering
     \includegraphics[width=\linewidth]{FiguresTables/pdf/sir2.pdf}
  \caption{}
  \label{Figure:fig_b}
\end{subfigure}

\medskip

\begin{subfigure}[t] {0.4\textwidth}
\centering
     \includegraphics[width=\linewidth]{FiguresTables/pdf/fob1.pdf}
  \caption{}
  \label{Figure:fig_c}
\end{subfigure}
%
\begin{subfigure}[t] {0.4\textwidth}
\centering
     \includegraphics[width=\linewidth]{FiguresTables/pdf/hxk2.pdf}
  \caption{}
  \label{Figure:fig_d}
\end{subfigure}


\begin{minipage}[t]{0.4\textwidth}
\caption{Try a multi-panel figure}
\end{minipage}

\end{figure}

\end{document}



See also: subcaption is more recent that subfigure or subfig
https://tex.stackexchange.com/questions/122314/figures-what-is-the-difference-between-using-subfig-or-subfigure

track changes in latex

https://gitlab.com/git-latexdiff/git-latexdiff

bibtex doi bug

in qin_network.bib, I added a reference with DOI field. This filed generates an error in *bbl file using $bibtex$.  I removed the DOI fileds and the bug disappeared.

bmc latex

BMC latex from its old website does not work (missing lastpage.sty)

Github latex seems to work, but missing some format features.

Biomed central tex tamplate, Github

http://old.biomedcentral.com/bmcsystbiol/authors/instructions/software

http://www.biomedcentral.com/authors/tex

Github latex template, cloned to QinLab.

Draw to look for latex symbol syntax

http://detexify.kirelabs.org/classify.html

Symbols in Latex.

Searchable html
http://www.artofproblemsolving.com/Wiki/index.php/LaTeX:Symbols
http://web.ift.uib.no/Teori/KURS/WRK/TeX/symALL.html

PubMed to BibTex

1. BibDesk through HubMed

BibDesk seems to run on Mac, Windows, and Linux.

2. Texmed
http://www.bioinformatics.org/texmed/

Copy-past from TexMed to *.bib files include "quotes". So, I have manually add the fields in BibDesk.

Useful Latex templates and tips

Draw and look for latex symbols
http://detexify.kirelabs.org/classify.html


http://www.plosone.org/static/latexGuidelines


Two column article with PDF figures
http://embedded.eecs.berkeley.edu/concurrency/latex/latexWithPDF.html

Latex template galleries
http://tex.stackexchange.com/questions/1362/latex-template-gallery

http://www.personal.ceu.hu/tex/cookbook.html

Latex for biologists
http://schneider.ncifcrf.gov/latex.html

Commands sequence
pdflatex templatePDF
bibtex templatePDF
pdflatex templatePDF
pdflatex templatePDF

Beamer Presentation
https://www.youtube.com/playlist?list=PL8013BD91081DC008

Latex for biologists
http://schneider.ncifcrf.gov/latex.html

Install TeX Live, TeXShop on an OS X mountain lion laptop

First, install TeXLive using port.


$ sudo port install texlive 
--->  Computing dependencies for texlive
--->  Dependencies to be installed: texlive-basic texlive-bin fontconfig ghostscript autoconf help2man p5.12-locale-gettext perl5.12 gdbm perl5 automake jbig2dec lcms2 libidn libpaper libpng libtool pkgconfig xorg-libXext xorg-xextproto xorg-libXt xorg-libsm xorg-libice libzzip poppler cairo glib2 libffi libpixman lzo2 xorg-xcb-util xrender xorg-renderproto curl curl-ca-bundle openjpeg jbigkit poppler-data t1lib texlive-common xorg-libXaw xorg-libXmu xpm xorg-libXp xorg-printproto texlive-documentation-base texlive-bin-extra detex dvipng gd2 latexdiff p5.12-algorithm-diff latexmk texlive-latex pdfjam texlive-latex-recommended pgf texlive-context texlive-fonts-recommended texlive-math-extra texlive-metapost texlive-xetex texlive-generic-recommended texlive-documentation-english texlive-fontutils lcdf-typetools ps2eps psutils t1utils texlive-lang-czechslovak texlive-lang-dutch texlive-lang-english texlive-lang-french texlive-lang-german texlive-lang-italian texlive-lang-polish texlive-lang-portuguese texlive-lang-spanish texlive-luatex
--->  Fetching archive for fontconfig
--->  Attempting to fetch fontconfig-2.10.2_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/fontconfig
--->  Attempting to fetch fontconfig-2.10.2_0.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/fontconfig
--->  Installing fontconfig @2.10.2_0
--->  Activating fontconfig @2.10.2_0
--->  Cleaning fontconfig
--->  Fetching archive for gdbm
--->  Attempting to fetch gdbm-1.10_2.darwin_12.x86_64.tbz2 from http://packages.macports.org/gdbm
--->  Attempting to fetch gdbm-1.10_2.darwin_12.x86_64.tbz2.rmd160 from http://packages.macports.org/gdbm
--->  Installing gdbm @1.10_2
--->  Activating gdbm @1.10_2
--->  Cleaning gdbm
--->  Fetching archive for perl5.12
--->  Attempting to fetch perl5.12-5.12.4_1.darwin_12.x86_64.tbz2 from http://packages.macports.org/perl5.12
... ...



Second, install the frontend TeXShop.

$ sudo port install Texshop3

--->  Fetching archive for TeXShop3

... ...

There are some link problem fo /usr/texbin/pdflatex.  So, 

$ sudo mkdir texbin

Password:

$ cd texbin/

$ sudo ln -s /opt/local//bin/pdflatex .

$ sudo ln -s /opt/local//bin/*latex* .