Package: barriers Version: 1.8.1-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 153 Depends: libc6 (>= 2.14), perl Filename: ./amd64/barriers_1.8.1-1_amd64.deb Size: 59960 MD5sum: ce2a67cbd451d2bb5409de866e1fd900 SHA1: 8ac45eb7d20c25852ff21b23f3a50d891c5efc67 SHA256: 8668b87739b3ed76885144de098c75c9f0a747947f22dd60ac6afede4694b1f0 Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Compute local minima and energy barriers of a landscape The program barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory. Package: barriers Version: 1.8.1-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 155 Depends: libc6 (>= 2.7), perl Filename: ./i386/barriers_1.8.1-1_i386.deb Size: 60228 MD5sum: dc0201ffe7e17ae4e92e9bd30d259d87 SHA1: f2d00b24c665c0fd3b02c301e693e5f44c666d01 SHA256: 5640b3cabe44bb36b3930efb971b38898f5b936059952e46aa3a4d4739994263 Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Compute local minima and energy barriers of a landscape The program barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For RNA secondary structures, suitable input is produced by RNAsubopt For each local minimum found it prints to stdout, the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation and basin sizes can be included via options. A PostScript drawing of the resulting tree is written to "tree.ps" in the current directory. Package: mlapack-dev Source: mlapack Version: 0.8.1-2 Architecture: amd64 Maintainer: Maho Nakata Installed-Size: 120428 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.3), libstdc++6 (>= 5.2), libgomp1, libquadmath0, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mlapack-dev Provides: mlapack-dev Filename: ./amd64/mlapack-dev_0.8.1-2_amd64.deb Size: 27138880 MD5sum: 67fc52359085b3642530b067431b93a4 SHA1: 51d16662d8ad34784f4586e136de953c801ff3a4 SHA256: e9a68d9f382a46ab76e8fcbc46e0d1b1e802f93ed6e1492db7ea98024fb10b5b Section: devel Priority: optional Description: mlapack - MPACK multi precision linear algebra package development files The MPACK is a multiprecision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: mlapack-dev Source: mlapack Version: 0.8.1-2 Architecture: i386 Maintainer: Maho Nakata Installed-Size: 102902 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4), libstdc++6 (>= 5.2), libgomp1, libquadmath0, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mlapack-dev Provides: mlapack-dev Filename: ./i386/mlapack-dev_0.8.1-2_i386.deb Size: 24777408 MD5sum: 0b99ceb17f856db2dc11c70aa5e2dd20 SHA1: 5b13fdb93a1da627fd6ce2708c1f01ced14f47e3 SHA256: 048ccf76e0c4846c8cbf7300abe3626f469d933a5e5f69b997c93cfb012d3c32 Section: devel Priority: optional Description: mlapack - MPACK multi precision linear algebra package development files The MPACK is a multiprecision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: mpack-dev Source: mpack Version: 0.8.0 Architecture: amd64 Maintainer: Gregor Entzian Installed-Size: 239752 Depends: libc6 (>= 2.14), libgcc1 (>= 1:4.3), libstdc++6 (>= 5.2), libquadmath0-dbg, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mpack-dev Provides: mpack-dev Filename: ./amd64/mpack-dev_0.8.0_amd64.deb Size: 52999072 MD5sum: 207330750e074c83c8887cde88914dba SHA1: b20d2ab669d2ea5afca7ce78d9d102e57e742b69 SHA256: 888ce45ceb04a283d712404e7394e4f9bdab160f8193fb02b193d9e64c926906 Section: devel Priority: optional Description: mpack - mpack development files The MPACK is a multipricision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: mpack-dev Source: mpack Version: 0.8.0 Architecture: i386 Maintainer: Gregor Entzian Installed-Size: 204634 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4), libstdc++6 (>= 5.2), libquadmath0-dbg, libgmp-dev, libmpfr-dev, libmpc-dev, libqd-dev Conflicts: mpack-dev Provides: mpack-dev Filename: ./i386/mpack-dev_0.8.0_i386.deb Size: 48802050 MD5sum: 9b0d931aa522708feedb11871291789b SHA1: 2f81a3de919b47032cfb9550861ffca7ceec1d5a SHA256: 99b81ae4fdaf3beb7f88b7e0c9e50b45a7185b7d94d3999b1745b35cc00fbf89 Section: devel Priority: optional Description: mpack - mpack development files The MPACK is a multipricision linear algebra package based on BLAS and LAPACK. This package is rewritten in C++, and supports several high precision libraries like GMP, MPFR and QD etc so that users can choose for user's convenience. The MPACK is a free software (2-clause BSD style license with original license by LAPACK). Package: perl-rna-barrier Source: barriers Version: 1.8.1-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 27 Depends: perl, perl-rna Filename: ./amd64/perl-rna-barrier_1.8.1-1_amd64.deb Size: 6584 MD5sum: ad573e84b8ae52bbda4e140c36b6bcbb SHA1: 9f7507a1ecfc4703f5ccfff8a1ba1fdafaf89241 SHA256: 075fdbe308b90c8e2a742518ae1802d72cb80e118d3fbc98c56378c89cf55285 Section: perl Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Perl module and scripts for Barriers The RNA/barrier module and perl scripts to access some functionality of the Barriers program Package: perl-rna-barrier Source: barriers Version: 1.8.1-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 27 Depends: perl, perl-rna Filename: ./i386/perl-rna-barrier_1.8.1-1_i386.deb Size: 6604 MD5sum: 99fd2545563160f28d767bc5b15e4fdc SHA1: 6595d76f622426365353dbbeb116b621abefcfdd SHA256: d96add5e89082874a276c970c11a976e059c81bd6156b5a7c3dd7ab5cbe3b286 Section: perl Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Perl module and scripts for Barriers The RNA/barrier module and perl scripts to access some functionality of the Barriers program Package: treekin Version: 0.5.0-1 Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 112 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), liblapack3, libstdc++6 (>= 4.9), libblas3, liblapacke, gfortran, mlapack-dev Filename: ./amd64/treekin_0.5.0-1_amd64.deb Size: 46064 MD5sum: 3aa959e7c373a2a1fb73f8daf7d99b1d SHA1: 89e99a0ab7fad8ed4cac38b1917f037855ca545f SHA256: fd3004d72a32558ca8823ed9d74590f1ab1bd87bdd6e5eb35d18a4702dbde96f Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Treekin Description: Efficient computation of RNA folding dynamics The program treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. Treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix). For detailed instructions see the man page. Package: treekin Version: 0.5.0-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 114 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.0), liblapack3, libstdc++6 (>= 4.9), libblas3, liblapacke, gfortran, mlapack-dev Filename: ./i386/treekin_0.5.0-1_i386.deb Size: 46698 MD5sum: 940c86f4322c00145016176eeb7aceff SHA1: c8cb75ddc4ead5daa437c90faa59b936b6a36361 SHA256: 1f7cb69f989b86f3eef6362760403e6d442360c803630f32b0c47c8a42496f4f Section: science Priority: optional Homepage: http://www.tbi.univie.ac.at/RNA/Treekin Description: Efficient computation of RNA folding dynamics The program treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. Treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix). For detailed instructions see the man page.