added some software names

Users/Saumon/Desktop/textbook/chapter_noncanonical/.gitignore

+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.log
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+.pdf
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa

Users/Saumon/Desktop/textbook/chapter_noncanonical/chapter_noncanonical.tex

+\documentclass[12pt]{article}
+
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+
+\usepackage{xspace}
+\usepackage{amsmath}
+\usepackage{url}
+\usepackage{todonotes}
+\usepackage{subcaption}
+\usepackage{natbib}
+\usepackage{dsfont}
+\usepackage{mdframed}
+
+
+\author{Roman Sarrazin-Gendron, J\'er\^ome Waldisp\"uhl, Vladimir Reinharz}
+\title{Non-canonical Base Pairs and Structural Motifs}
+\date{}
+
+\begin{document}
+	\maketitle
+	
+	\section{Non-canonical base pairs}
+		\begin{mdframed}
+			\begin{itemize}
+				\item Leontis-Westhof annotations (I'll adapt my previous figure)
+				\item FR3D
+				\item MCAnnotate
+				\item claRNA
+				\item RNAVIEW/RNAMLVIEW
+				\item forgi?
+				
+			\end{itemize}
+		\end{mdframed}
+
+	
+	\section{Non-canonical motifs}
+		\begin{mdframed}
+			\begin{itemize}
+				\item RNA3DMotif
+				\item RNA 3D Motif Atlas
+				\item RNABricks
+				\item CaRNAval
+				\item RNAMotifScan
+			\end{itemize}
+		\end{mdframed}
+		
+
+	\section{Methods}
+		\begin{mdframed}
+			\begin{itemize}
+				\item Small review, based on sequence, RMdetect, JAR3D, metaRNAmodules etc...
+				\item most of the chapter on BayesPairing
+			\end{itemize}
+		\end{mdframed}
+
+\end{document}
\ No newline at end of file