Package: barriers Version: 1.8.1-1 Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 164 Depends: libc6 (>= 2.7), perl Filename: ./i386/barriers_1.8.1-1_i386.deb Size: 64606 MD5sum: ad9e93cb47f09e5ce313bb45729867db SHA1: 8596b6713513826d1c93d875060b752a99eefb57 SHA256: 88426564c9612ca80fa51a864d0f37fa81524e4120476f1e62ce2c73f870b3b3 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: amd64 Maintainer: Ronny Lorenz Installed-Size: 158 Depends: libc6 (>= 2.14), perl Filename: ./amd64/barriers_1.8.1-1_amd64.deb Size: 61468 MD5sum: 9e48b874820eb9236e21aaafdbff0ea2 SHA1: 3a1f465cce7830368d426244054c02d48c38bed5 SHA256: b24eae4dbc7ebabf51d26048b9d74133ebf15ff8b574ef8f9af3101b2d14227c 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-dbgsym Source: barriers Version: 1.8.1-1 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 117 Depends: barriers (= 1.8.1-1) Filename: ./i386/barriers-dbgsym_1.8.1-1_i386.deb Size: 96052 MD5sum: 5da44efe5a136280c73ec9220b648f3e SHA1: 95ad0f188500b9786ed5a9eb05460e716caed7a0 SHA256: 6c390f13278097e41f4af0f652a959e505908eaad5e267a73cff0131292f6073 Section: debug Priority: extra Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Debug symbols for barriers Build-Ids: 60493767e1070a349f3f1f227059a6d7f13ff269 f24ef3ec76e715d2c138ffaba91a7706617579c0 Package: barriers-dbgsym Source: barriers Version: 1.8.1-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 131 Depends: barriers (= 1.8.1-1) Filename: ./amd64/barriers-dbgsym_1.8.1-1_amd64.deb Size: 103990 MD5sum: 63157f140d5883f1775aba5c51328f84 SHA1: 5b4b41a8e22d168979354ec470024da5eda142a9 SHA256: df10faffc75a207d103dd02831ed2ccd4995910eae1fbb44774299b8cd8939cd Section: debug Priority: extra Homepage: http://www.tbi.univie.ac.at/RNA/Barriers Description: Debug symbols for barriers Build-Ids: 025eb3bed9e1b3030fb123a63816335393aa8809 708829b815a88d0516f8870642bd113b5fca25d7 Package: mlapack-dev Source: mlapack Version: 0.8.1-2 Architecture: i386 Maintainer: Maho Nakata Installed-Size: 108234 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: 19904520 MD5sum: 97b8559875c5306b7380534beb70a82d SHA1: 88246ae851a57f23752ab56c8383061269f7428c SHA256: 627fd1817661688a79783353b0192e5e65031de6eef363a95720eaff2e3acbf2 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: amd64 Maintainer: Maho Nakata Installed-Size: 119778 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: 22860938 MD5sum: 9160f2b848403acab7ade6d1bbba062a SHA1: b54912f9ed9613c440c702ed0d9dd579bb1bae5c SHA256: b1d707470d45a14251d241b128dc814d39bc0eee04eb2b7639ce7118fb09b93e 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-dbgsym Source: mlapack Version: 0.8.1-2 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Maho Nakata Installed-Size: 79483 Depends: mlapack-dev (= 0.8.1-2) Filename: ./i386/mlapack-dev-dbgsym_0.8.1-2_i386.deb Size: 78384104 MD5sum: 775487c30c03deeb6ec18d32c309b807 SHA1: 1b818995c880a216c09b9b0727d71b53e7b7a7f4 SHA256: dfc40201922a74473cd58b1f4d920e8a7eb228ae652cdaee0e13a7d843f5b205 Section: debug Priority: extra Description: Debug symbols for mlapack-dev Build-Ids: 2893e5ebbf2a3f852008d71bc77b6fd3bc34b8fe 334effbb9b0aba305433a11643eb0edd94aac348 3ca094cb49414a3c769a59fa6c87a7e28e61c8e5 4fa994872a9352c0ac63dfcb8022be09db1642d0 52ad4a4c145e25af86b01806780b59c1b1fb21ac 5e0f42cf148cdb5cde725ce992d418f7245d4b53 69e72b3be53ee9e9edd8dca04a42ca22f6db318d 6dfd687717a6ab53277a40141b3d5140537a92bf 75ae84a511236c4ecbf6ecd0ada4d8394198f014 bfe2a13cb5684358b3420c6789673c7795647170 ddda00030ec6c7ecdd57af826544544129d51637 e339af2ba8d68d148f3fec0be16b8ad24858fd27 e94a8794f8877b75e77c7c8469a65a4938add6b6 f09e681061b3615a2ab6fd12a5b8a8de69c6dec6 f58702c8a655e7d559597a596decf06ab765aca7 Package: mlapack-dev-dbgsym Source: mlapack Version: 0.8.1-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Maho Nakata Installed-Size: 91562 Depends: mlapack-dev (= 0.8.1-2) Filename: ./amd64/mlapack-dev-dbgsym_0.8.1-2_amd64.deb Size: 90373432 MD5sum: 6877d5aa3d805a31702b6d7faf29c53e SHA1: 863980a9ea531d314c8069d679d015aac33d3edc SHA256: 6b88d71edb884601e3800e0e4bc44f239b80e2a54d7ecc466f194e3f9f22f23d Section: debug Priority: extra Description: Debug symbols for mlapack-dev Build-Ids: 06c80a5cae482ee9fef5a2ce853a237a3ac1bfc4 15837cdb9363ba02dbc9ff642142d240a0f03202 1b981d1dfdb4fba02996eac2311a94685d2df233 27522133045b874938ca2209d6d3eb32e1f28a49 3557bec5aea34be5de098824d7d3374f76a9fd8b 390030a3de27d198c5b291acca701c78af2fafd4 5893cd6906b9363bf68ecf4a124355ba59a4aa45 812fe07556c7d49e6cfe11f9d29f6b242c952d47 82e1ba9fd72a969e3148f26e4486a9546adfd6f3 855582edf98fff88a70a83b71b8818551abb559b a650eab87fb47e1f27c6c6ad289b596a8b934f0d ba4e7c69529f8f19048ac42579836f6a6280d601 bab23516ef112b077f816f5d0d8d4142b89ee8b6 da437a8ff3d9c5c6035dd8a1b4ee009b13fbb80a e48235d9d88cbf676693c5fcc174ae7db6eed708 Package: mpack-dev Source: mpack Version: 0.8.0 Architecture: i386 Maintainer: Gregor Entzian Installed-Size: 215243 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: 35604794 MD5sum: 2b97a1380b87a978a14b95d6a42048e4 SHA1: c428ab2f216f8848ede0fbadc2d3c6722c9d6fdc SHA256: 2e91c417b975a2e0e5d36967ac177640d9afc87a6ee18681697fef4755b15e37 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: amd64 Maintainer: Gregor Entzian Installed-Size: 237972 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: 40959116 MD5sum: 0e9c3bc41b445058298e0975285d2c7e SHA1: 08fd8ee189845e363e63831a78cf6ada340ea637 SHA256: 44ff83e3e7295f76e8f81ad6a8fc85bcaa310f84ea1a265ef07b261dbe344b07 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: i386 Maintainer: Ronny Lorenz Installed-Size: 28 Depends: perl, perl-rna Filename: ./i386/perl-rna-barrier_1.8.1-1_i386.deb Size: 7516 MD5sum: 8f0bb959fe496f2f8d8986a080cdefb0 SHA1: 5b75f7b016268cb7f3eca2a254f52e0439d2ee4d SHA256: 7f84a8e5a33a2522f45cc24d18eb3ab148d7691332f657da2419e676d1402763 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: amd64 Maintainer: Ronny Lorenz Installed-Size: 28 Depends: perl, perl-rna Filename: ./amd64/perl-rna-barrier_1.8.1-1_amd64.deb Size: 7518 MD5sum: 47da62e8392e0cf9f29226d7a9a7e4d0 SHA1: dcebbca324b1a6f664aad54cb7eaab4fc5931bfc SHA256: 58614918d9c23572503c8ed28892e467af10b4bd1aba92a8d4a25c8329eb0eaf 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: i386 Maintainer: Ronny Lorenz Installed-Size: 119 Depends: libblas3, libc6 (>= 2.4), libgcc1 (>= 1:3.0), libgfortran3 (>= 4.3), liblapack3, libquadmath0 (>= 4.6), libstdc++6 (>= 4.9), liblapacke, gfortran, mlapack-dev Filename: ./i386/treekin_0.5.0-1_i386.deb Size: 50262 MD5sum: 08eb3aad7d8227c1bde5261cfdea71cc SHA1: ffe9ca82b4cfe94d23790b1d1bb91be0a389930e SHA256: 2dd898b0f4e062686996f23831a4ba888557ee01d85e0083e5809adb36497c85 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: amd64 Maintainer: Ronny Lorenz Installed-Size: 117 Depends: libblas3, libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgfortran3 (>= 4.3), liblapack3, libquadmath0 (>= 4.6), libstdc++6 (>= 4.9), liblapacke, gfortran, mlapack-dev Filename: ./amd64/treekin_0.5.0-1_amd64.deb Size: 47894 MD5sum: 8591efae58862b687dd72a133274cca2 SHA1: 532b6b7588773c8a72d671a5cd39c784608cb0d2 SHA256: 138edea2eb6ca85831238c43d61c50c1609905434e50f16bc614ff8461a64c10 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-dbgsym Source: treekin Version: 0.5.0-1 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Ronny Lorenz Installed-Size: 181 Depends: treekin (= 0.5.0-1) Filename: ./i386/treekin-dbgsym_0.5.0-1_i386.deb Size: 165180 MD5sum: 23df7d8a0b39bb8e8f540d2725cadb9b SHA1: df50e36146451f549abac34dcf424ed3038a8772 SHA256: 018734cef8e0e0c4e5f9b53db67f4b22aaf464d7089d8d1a53f08e534bd4e794 Section: debug Priority: extra Homepage: http://www.tbi.univie.ac.at/RNA/Treekin Description: Debug symbols for treekin Build-Ids: a502dd7bac606b1b974689fcdef1456fcdf91301 Package: treekin-dbgsym Source: treekin Version: 0.5.0-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Ronny Lorenz Installed-Size: 188 Depends: treekin (= 0.5.0-1) Filename: ./amd64/treekin-dbgsym_0.5.0-1_amd64.deb Size: 171432 MD5sum: 238b39b244e0adc261f35bcf1064d52a SHA1: 219a6f3ba9b4333c10439814040496afea9b0d38 SHA256: 98449ee7f92cd16b48c589a5bc91b87a836f95302444ecd8dd5a1a112e9603b2 Section: debug Priority: extra Homepage: http://www.tbi.univie.ac.at/RNA/Treekin Description: Debug symbols for treekin Build-Ids: bd0dc18950162c092ce43e937ca6025bf02b33ce