This template is created based on Thesis requirements of NCBS-TIFR.

• main.tex : Standalone file which will combine all aspects of the thesis. You can customize view and arrangement of thesis from this file
• main_ref.bib : All bibliography (you can have multiple files as well. Just change details in helpers\bib.tex)
• front_matter\ : Includes all front matter files like declarations, certificate etc.
• chapters\ : Includes all chapters. To organize better, keep separate document for each chapter.
• figs\ : All figures
• helpers\ : Acronyms and bibliography helper file
• appendix\ : Appendices
• script.bat : Compilation script (for Windows)

To compile all the structures (with pdflatex), follow following procedure

Note: Initial compilation might take long time if you do not have all the latex packages needed to compile. Before compiling check if you have all the packages installed. You can switch on automatic package installation if using MikTex. 

Just run script.bat (double click it)

use following procedure. You can check sample code in script.bat.

1. First Compile once to generate .idx file
2. Make index from .idx file with makeindex command
3. Make .acn and .acr files from output produced from makeindex
4. Run bibtex on all .aux files produced (all chapters and appendix will produce separate .aux file to have separate bibliography)
5. Run pdflatex twice

to create index run

makeindex  main.nlo -s nomencl.ist -o  main.nls

to create glossary run

makeindex -s main.ist -t main.alg -o main.acr main.ac

To include separate references for each chapter, natbib and chapterbib packages are used. To use these packages, we have to add chapter files as "\include{}" instead "\input{}". Also we need to compile each chapter aux file seperately. We also need to include biblography in every chapter. It will follow this sequence,

pdflatex main.tex
bibtex chapter1.aux
bitbex chapter2.aux ... and so on
pdflatex main.tex
pdflatex main.tex