merge(999.70-01): TUT-01 tutorial.tex refresh — URLs, release tag, roster, citation

- Refresh outbound URLs (http->https ball-project.org; dead pdb4pti.ent path),
  release tag, and build-doc pointers (build steps already removed per #560).
- Update author/developer roster + add canonical BMC 2010 citation to tutorial.bib.
TUT-01 PDF render + screenshot recapture remain Wave-2 (human, plan 999.70-03).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: okohlbacher

doc/TUTORIAL/example4.tex

@@ -9,15 +9,15 @@ \section{The BALL File Class}
 
 \begin{lstlisting}{}
   PDBFile
-  infile("http://www.ball-project.org/Downloads/Examples/pdb4pti.ent");
+  infile("https://files.rcsb.org/download/4PTI.pdb");
   System S;
   infile >> S;
   infile.close();
 \end{lstlisting}
 
 \noindent
-This command retrieves the file {\tt pdb4pti.ent} from its location at the BALL
-project site using the HTTP protocol and reads the contents of that file into a
+This command retrieves the PDB entry {\tt 4PTI} directly from the RCSB Protein
+Data Bank using the HTTP protocol and reads the contents of that file into a
 \class{System}. The retrieval and the expansion of the URL into something
 meaningful is performed by the classes \class{TransformationManager} and
 \class{TCPTransfer}. Any filename is first handed to the static instance of

doc/TUTORIAL/faq.tex

@@ -1,20 +1,20 @@
 \FAQCategory{Documentation}
 \FAQquestion{Are there Research reports available?}
-\FAQanswer{Yes. Publications and research reports on BALL are listed on our website: 
-\FAQURL{http://www.ball-project.org}
+\FAQanswer{Yes. Publications and research reports on BALL are listed on our website:
+\FAQURL{https://ball-project.org}
 }
 \FAQquestion{Where do I get the latest version?}
-\FAQanswer{The latest version of BALL, bug fixes, and updates are available from our 
-website
-\FAQURL{http://www.ball-project.org}
+\FAQanswer{Pre-built BALLView packages for macOS, Windows, and Linux are published on the
+GitHub Releases page
+\FAQURL{https://github.com/BALL-Project/ball/releases/latest}
 }
 \FAQquestion{Is there further documentation besides this document?}
-\FAQanswer{Further documentation, a Wiki and a bug tracker, can be found on 
+\FAQanswer{Further documentation, a Wiki and a bug tracker, can be found on
 \FAQURL{https://github.com/BALL-Project/ball/}
 providing a Code Library with Code snippets, further tutorials, Release Notes, and FAQs.
 }
 \FAQquestion{How do I use BALLView?}
-\FAQanswer{Take a look at the built-in BALLView Tutorial or on the documentation at http://www.ball-project.org/Documentation}
+\FAQanswer{Take a look at the built-in BALLView Tutorial or at the project wiki at \FAQURL{https://github.com/BALL-Project/ball/wiki}}
 \FAQCategory{Installation}
 \FAQquestion{Will BALL run on my hardware/with my compiler?}
 \FAQanswer{BALL should run on all major current platforms, in particular Linux, MacOS X, and Windows. Older BALL

doc/TUTORIAL/introduction.tex

@@ -11,22 +11,36 @@
 Manual}~\cite{BALL-RM} which can be obtained in HTML, PDF, or postscript format.
 
 There are also several papers and technical reports published on
-BALL~\cite{BKL99a,BKL99b,KL99,Koh2001,KL2000,MHLK05,MHLK06}
+BALL~\cite{Hildebrandt2010BALL,BKL99a,BKL99b,KL99,Koh2001,KL2000,MHLK05,MHLK06}
 that give a cursory overview of its design principles and illustrate its use in
-Rapid Software Prototyping. If you publish results that were obtained using 
+Rapid Software Prototyping. If you publish results that were obtained using
 BALL, please cite it as follows:
 \begin{enumerate}
+  \item[] A. Hildebrandt, A. K. Dehof, A. Rurainski, A. Bertsch,
+          M. Schumann, N. C. Toussaint, A. Moll, D. St\"{o}ckel,
+          S. Nickels, S. C. M\"{u}ller, H.-P. Lenhof, O. Kohlbacher:
+          BALL -- Biochemical Algorithms Library 1.3,
+          {\em BMC Bioinformatics} 2010, 11:531
+          (DOI: 10.1186/1471-2105-11-531).
   \item[] O. Kohlbacher, H.-P. Lenhof: BALL -- Rapid Software Prototyping
           in Computational Molecular Biology, {\em Bioinformatics} 2000,
           16(9):815--824.
 \end{enumerate}
 
 \noindent
-The latest version of BALL, bug fixes, and updates are available from our 
+The latest version of BALL, bug fixes, and updates are available from our
 website
 
 \begin{enumerate}
-  \item[] \URL{http://www.ball-project.org}.
+  \item[] \URL{https://ball-project.org}
+\end{enumerate}
+
+\noindent
+Pre-built BALLView packages for macOS, Windows, and Linux are published on the
+GitHub Releases page
+
+\begin{enumerate}
+  \item[] \URL{https://github.com/BALL-Project/ball/releases/latest}
 \end{enumerate}
 
 \noindent

doc/TUTORIAL/tutorial.bib

@@ -1,5 +1,19 @@
+@article{Hildebrandt2010BALL,
+  author       = {Hildebrandt, A. and Dehof, A. K. and Rurainski, A.
+                  and Bertsch, A. and Schumann, M. and Toussaint, N. C.
+                  and Moll, A. and St\"{o}ckel, D. and Nickels, S.
+                  and M\"{u}ller, S. C. and Lenhof, H.-P.
+                  and Kohlbacher, O.},
+  title        = {{BALL} -- {B}iochemical {A}lgorithms {L}ibrary 1.3},
+  journal      = {BMC Bioinformatics},
+  year         = {2010},
+  volume       = {11},
+  pages        = {531},
+  doi          = {10.1186/1471-2105-11-531},
+}
+
 @inproceedings{BKL99b,
-  author       = {Boghossian, N. P. and Kohlbacher, O. and Lenhof, H.-P.}, 
+  author       = {Boghossian, N. P. and Kohlbacher, O. and Lenhof, H.-P.},
   editor       = {Vitter, J. S. and Zaroliagis, C. D.},
   title        = {{BALL}: {B}iochemical {A}lgorithms {L}ibrary},
   booktitle    = {Algorithm Engineering, 3rd International Workshop, {WAE}'99,

doc/TUTORIAL/tutorial.tex

@@ -1,8 +1,12 @@
 \documentclass[12pt,twoside]{report}
 
 \author{
-  Oliver Kohlbacher, Heiko Klein, Andreas Kerzmann, \\
-  Andreas Moll, Andreas K\"{a}mper, Anna Katharina Dehof, Andreas Hildebrandt
+  Andreas Hildebrandt, Anna Katharina Dehof, Alexander Rurainski, \\
+  Andreas Bertsch, Marcel Schumann, Nora C. Toussaint, Andreas Moll, \\
+  Daniel St\"{o}ckel, Stefan Nickels, Sabine C. M\"{u}ller, \\
+  Heiko Klein, Andreas Kerzmann, Andreas K\"{a}mper, \\
+  Hans-Peter Lenhof, Oliver Kohlbacher
+  % TODO(999.70): confirm current maintainer roster
 }
 \title{
   \begin{center}
@@ -12,7 +16,7 @@
   \Large A Tutorial
 }
 \date{
-  Release 1.7\\
+  Release 1.7.4\\
   \today
 }