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docs(999.70-01): refresh tutorial URLs, release tag, build-doc + citation pointers
- tutorial.tex: release tag Release 1.7 -> Release 1.7.4 - introduction.tex: http://www.ball-project.org -> https://ball-project.org; downloads pointer now to GitHub Releases (releases/latest); add canonical BMC Bioinformatics 11:531 (2010) citation as primary 'please cite' reference - example4.tex: dead http://www.ball-project.org/Downloads/Examples/pdb4pti.ent -> live https://files.rcsb.org/download/4PTI.pdb (RCSB PDB) - faq.tex: http:// project URLs -> https://; latest-version pointer to GitHub Releases; /Documentation pointer -> project wiki - All tutorial URLs verified 200; no inline build steps (removed per #560) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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doc/TUTORIAL/example4.tex

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

doc/TUTORIAL/faq.tex

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

doc/TUTORIAL/introduction.tex

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

doc/TUTORIAL/tutorial.tex

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\Large A Tutorial
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}
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\date{
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Release 1.7\\
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Release 1.7.4\\
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\today
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}
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