| 1 | /******************************************************************************* |
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| 2 | * ProMoT |
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| 3 | * --------------------------------------------------------------------------- |
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| 4 | * Copyright (c) 1997-2012 ProMoT Development Team |
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| 5 | * Max Planck Institute Magdeburg, Germany |
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| 6 | * http://www.mpi-magdeburg.mpg.de/projects/promot |
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| 7 | * |
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| 8 | * This is free software; you can redistribute it and/or modify it |
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| 9 | * under the terms of the GNU General Public License as published |
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| 10 | * by the Free Software Foundation; either version 2 of the License, or |
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| 11 | * any later version. |
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| 12 | * |
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| 13 | * THIS SOFTWARE IS DISTRIBUTED IN THE HOPE THAT IT WILL BE USEFUL, |
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| 14 | * BUT WITHOUT ANY WARRANTY; WITHOUT EVEN THE WARRANTY OF |
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| 15 | * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. |
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| 16 | * IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE |
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| 17 | * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL |
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| 18 | * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS |
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| 19 | * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) |
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| 20 | * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT |
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| 21 | * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY |
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| 22 | * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF |
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| 23 | * SUCH DAMAGE. |
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| 24 | * |
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| 25 | * You should have received a copy of the GNU General Public License |
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| 26 | * along with this library; if not, write to the Free Software Foundation, |
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| 27 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. |
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| 28 | * |
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| 29 | * --------------------------------------------------------------------------- |
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| 30 | * $Id$ |
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| 31 | ******************************************************************************/ |
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| 32 | |
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| 33 | ------------------------------------------------------------------- |
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| 34 | v-0-4-0 |
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| 35 | ------------------------------------------------------------------- |
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| 36 | - Initial revision of PROMOT version 4 |
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| 37 | - PROMOT ported to CVS |
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| 38 | |
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| 39 | - Object-oriented language definition of MDL |
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| 40 | - New version of FrameTalk (weak, strong parts, link-from) |
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| 41 | |
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| 42 | ------------------------------------------------------------------- |
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| 43 | v-0-4-1 |
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| 44 | ------------------------------------------------------------------- |
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| 45 | - `Component' renamed to `module' |
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| 46 | |
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| 47 | ------------------------------------------------------------------- |
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| 48 | v-0-4-2 |
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| 49 | ------------------------------------------------------------------- |
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| 50 | - mexpr.lisp: CG parser extended to slot paths |
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| 51 | - In mexprs. variables are no longer represented as objects, but as |
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| 52 | instances of slot-path. |
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| 53 | - promot-link introduced. |
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| 54 | The command option `:links' is no longer mapped to FDL. |
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| 55 | promot-link is rather used as strong parts. |
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| 56 | This led to major changes in the generation of link equations. |
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| 57 | |
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| 58 | ------------------------------------------------------------------- |
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| 59 | v-0-4-3 |
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| 60 | ------------------------------------------------------------------- |
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| 61 | - mdl.lisp: bug fixed when generating weak parts for mexprs in indices |
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| 62 | - format-mexpr.lisp: now also generates LaTeX code |
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| 63 | - First steps to implement module arrays |
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| 64 | |
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| 65 | ------------------------------------------------------------------- |
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| 66 | v-0-4-4 |
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| 67 | ------------------------------------------------------------------- |
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| 68 | - First version of implementing terminal arrays: |
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| 69 | This implementation is not based on FDL slot arrays. |
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| 70 | It does not allow the splitting of terminal arrays into single terminals, |
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| 71 | which is a must! |
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| 72 | |
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| 73 | ------------------------------------------------------------------- |
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| 74 | v-0-4-4 |
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| 75 | ------------------------------------------------------------------- |
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| 76 | - Fixed bug in sort-dependency-p (model.lisp). |
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| 77 | - The call to sort-dependency-p was not symmetric. |
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| 78 | |
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| 79 | ------------------------------------------------------------------- |
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| 80 | v-0-4-5 |
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| 81 | ------------------------------------------------------------------- |
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| 82 | - Removed sort-dependency-p. |
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| 83 | - Sorting variables according to their dependencies with LISP `sort' |
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| 84 | was buggy. |
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| 85 | - Reason: If a>b and b>c, it cannot be concluded that a>c! |
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| 86 | - Now: 1) the dependency lists of all variables are agglomerated |
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| 87 | 2) the total dependency graph is traversed by depth-first search |
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| 88 | 3) the nodes that are traversed last are printed first |
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| 89 | + additional alphabetic sorting of `all-direct-variables' in |
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| 90 | `dependency-list' (roots-mixins.lisp) |
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| 91 | |
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| 92 | ------------------------------------------------------------------- |
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| 93 | v-0-4-6 |
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| 94 | ------------------------------------------------------------------- |
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| 95 | - Coupling, propagation of vector terminals now running for |
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| 96 | - Two-phases, three-phases in kb/test-arrays.mdl |
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| 97 | - For this: model-name determination completely revised |
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| 98 | - path-indices-* methods introduced |
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| 99 | - Module arrays now running, at least for all modules in `test-arrays.mdl' |
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| 100 | - Terminal arrays now running, at least for all modules in `test-arrays.mdl' |
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| 101 | - Complete revision of |
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| 102 | - roots-mixins.lisp: path-indices-* |
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| 103 | - model.lisp: model-direct-identity-equations |
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| 104 | - Lots of other changes, bug fixes, I can't remember |
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| 105 | |
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| 106 | ------------------------------------------------------------------- |
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| 107 | v-0-4-7 |
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| 108 | ------------------------------------------------------------------- |
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| 109 | - Output of variables with :report attribute |
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| 110 | Now uses :x-scope, :y-scope, :z-scope in define-process-values |
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| 111 | |
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| 112 | ------------------------------------------------------------------- |
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| 113 | v-0-5-0 |
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| 114 | ------------------------------------------------------------------- |
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| 115 | - src/graphics/*: |
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| 116 | First new version of PROMOT Model Editor that runs with FDL |
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| 117 | - src/kernel/cg.lisp: |
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| 118 | Better formatting of CG file (Stefan Schwarzkopf) |
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| 119 | - images/Makefile created |
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| 120 | - kb/test-suite created for testing new PROMOT versions |
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| 121 | - Lots of bug fixes |
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| 122 | |
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| 123 | ------------------------------------------------------------------- |
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| 124 | v-0-5-1, 1998-06-04 |
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| 125 | ------------------------------------------------------------------- |
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| 126 | - src/kernel/format-mexpr.lisp: |
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| 127 | Bug fixed when formatting :cond |
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| 128 | - src/kernel/roots-mixins.lisp: |
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| 129 | Real and integer parameters are no longer indexed within indexed |
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| 130 | modules |
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| 131 | |
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| 132 | ------------------------------------------------------------------- |
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| 133 | v-0-5-2, 1998-06-16 |
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| 134 | ------------------------------------------------------------------- |
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| 135 | - src/kernel/cg.lisp: |
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| 136 | format-cg-commands improved |
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| 137 | - src/kernel/browser-interface.lisp |
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| 138 | src/kernel/mdl.lisp |
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| 139 | src/kernel/utilities.lisp |
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| 140 | src/graphics/browser.lisp |
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| 141 | src/graphics/editor.lisp |
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| 142 | src/graphics/mdl-command-viewer.lisp |
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| 143 | src/graphics/mdl-command-emacs.lisp: |
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| 144 | MDL commands are formatted in a pretty way for output to command viewer, |
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| 145 | EMACS or file |
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| 146 | - src/kernel/mdl.lisp: interprete |
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| 147 | Mixins of FDL part slot are now sorted alphabetically to avoid |
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| 148 | circular class precedence lists |
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| 149 | - src/kernel/optimize.lisp: NEW |
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| 150 | - Substitute variables rather than generating coupling equations |
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| 151 | - Substitution of state variables in mexpressions of help variables does |
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| 152 | not work in general, because of wrong pattern initialization. |
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| 153 | e.g., pattern is out of bounds in ba-process.cg |
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| 154 | |
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| 155 | ------------------------------------------------------------------- |
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| 156 | v-0-5-3 |
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| 157 | ------------------------------------------------------------------- |
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| 158 | - src/kernel/cg.lisp: |
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| 159 | bug fixed in format-cg-cmd-obj for process-values |
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| 160 | |
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| 161 | ------------------------------------------------------------------- |
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| 162 | v-0-5-4, 1998-09-25 |
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| 163 | ------------------------------------------------------------------- |
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| 164 | - Version as of SFB-412 evaluation - report for funding period 1996-1998 |
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| 165 | - Presentation of kb/hafke/obertopp and kb/distillation (tmm-process, ba-process) |
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| 166 | - src/kernel/utilities.lisp: |
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| 167 | print-class-tree writes class tree to stdout |
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| 168 | - src/kernel/editor-interface.lisp: |
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| 169 | set-diva-file-names modifies the keywords |
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| 170 | :diva-cg-file-name, :diva-fortran-files-subname, :diva-data-file-name |
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| 171 | and :diva-latex-file-name of a module; |
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| 172 | write-diva-files writes CG files and calls the CG |
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| 173 | - src/kernel/mdl.lisp: |
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| 174 | The keywords :diva-cg-file-name, :diva-fortran-files-subname, |
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| 175 | :diva-data-file-name and :diva-latex-file-name have been added to |
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| 176 | define-module |
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| 177 | - src/kernel/roots-mixins.lisp: |
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| 178 | The slots for :diva-cg-file-name, :diva-fortran-files-subname, |
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| 179 | :diva-data-file-name and :diva-latex-file-name have been added to |
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| 180 | promot-class-mixin; |
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| 181 | modified method cg-filename to determine the default CG filename of a module |
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| 182 | - src/graphics/*.lisp: |
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| 183 | Model output to DIVA added |
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| 184 | |
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| 185 | ------------------------------------------------------------------- |
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| 186 | v-0-5-5, 1998-11-03 |
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| 187 | ------------------------------------------------------------------- |
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| 188 | - src/graphics/editor.lisp, model-editor.lisp: added output to EPS file |
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| 189 | - Martin Ginkel starts working on ProMoT |
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| 190 | - Help variables are no longer written as indexed CG-help variables in the |
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| 191 | case of indexed modules. They are rather multiply assigned in equation |
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| 192 | loops. |
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| 193 | - Support of ACL 5.0 added. |
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| 194 | src/kernel/error.lisp and src/kernel/mdl.lisp: without-package-locks |
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| 195 | added because of use of symbols class and type |
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| 196 | - Bug fixed in src/kernel/roots-mixins.lisp: path-indices |
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| 197 | Do not generate indices in model name if |
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| 198 | a variable (strong part of a module) |
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| 199 | has been propagated to an indexed terminal. Example: kb/bio/speicher-neu.mdl |
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| 200 | |
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| 201 | ------------------------------------------------------------------- |
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| 202 | v-0-5-5-0 |
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| 203 | ------------------------------------------------------------------- |
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| 204 | - Inserted a branch into CVS to keep a clean working version |
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| 205 | This should be a mostly bugfree release, without new errors from |
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| 206 | the new GUI development. |
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| 207 | |
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| 208 | |
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| 209 | ------------------------------------------------------------------- |
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| 210 | v-0-5-6, 1999-01-07 |
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| 211 | ------------------------------------------------------------------- |
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| 212 | - Development release |
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| 213 | - src/kernel/mdl2diva reports errors correctly |
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| 214 | - src/kernel/optimize.lisp does the job of optimizing linked |
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| 215 | state-variables to help-variables in most cases. For safety reasons |
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| 216 | it is optional to do this |
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| 217 | - The Project for the GUI in Java/JFC with connection via ILU has |
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| 218 | been started |
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| 219 | - Volker Padur has joined the team, he develops the Java part |
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| 220 | |
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| 221 | ------------------------------------------------------------------- |
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| 222 | v-0-6-0, 2000-06-20 |
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| 223 | ------------------------------------------------------------------- |
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| 224 | - The optimizer is broken due to new structures in the kernel |
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| 225 | - errors.lisp has been renamed into conditions.lisp because |
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| 226 | we use conditions now for error reporting |
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| 227 | - The principle of using FDL has changed. ProMoT implements now it's |
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| 228 | own superclasses. this should be extended for the interactive |
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| 229 | editing of classes without using MDL. |
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| 230 | - The Java GUI has now almost the same functionality as the Clim one |
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| 231 | - Clim is still possible but I will stop the development on it |
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| 232 | - Images and scripting is now written to run almost automatical |
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| 233 | |
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| 234 | ------------------------------------------------------------------- |
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| 235 | v-0-6-0-0 |
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| 236 | ------------------------------------------------------------------- |
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| 237 | - New stable version instead of v-0-5-5 |
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| 238 | - Optimizer is ok now |
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| 239 | - Emacs and Java should work together through the old interface |
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| 240 | - Still some bugs in the GUI |
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| 241 | |
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| 242 | ------------------------------------------------------------------- |
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| 243 | v-0-7-0, 2004-11-09 |
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| 244 | ------------------------------------------------------------------- |
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| 245 | - |
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| 246 | |
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| 247 | ------------------------------------------------------------------- |
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| 248 | v-0-7-1, 2005-05-12 |
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| 249 | ------------------------------------------------------------------- |
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| 250 | - |
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| 251 | |
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| 252 | ------------------------------------------------------------------- |
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| 253 | v-0-7-2, 2006-08-16 |
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| 254 | ------------------------------------------------------------------- |
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| 255 | - Stable version with new features |
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| 256 | - SBML support matures |
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| 257 | - Diana output is fully functional |
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| 258 | - Support for structural models |
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| 259 | - Visual exploration of models |
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| 260 | - Graphical editing of variable values |
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| 261 | |
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| 262 | ------------------------------------------------------------------- |
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| 263 | v-0-8-0, 2008-02-22 |
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| 264 | ------------------------------------------------------------------- |
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| 265 | - Many extensions in the GUI |
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| 266 | - Undo for many commands |
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| 267 | - Automated layout and model documentation |
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| 268 | - Automated consistency checking |
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| 269 | |
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| 270 | ------------------------------------------------------------------- |
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| 271 | v-0-8-1, 2008-08-15 |
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| 272 | ------------------------------------------------------------------- |
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| 273 | - Import of CNA (CellNetAnalyzer) models |
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| 274 | - Bug fixes in generation of HTML documentation |
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| 275 | - (Partial) bug fix for renaming of connected slots (see BUGS.txt for limitations) |
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| 276 | - Modularization support in visual editing |
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| 277 | - Bug fixes in the variable editor |
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| 278 | - Support for import and export of layout information in the ProMoT Explorer |
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| 279 | - Windows version (since September 2008) |
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| 280 | |
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| 281 | ------------------------------------------------------------------- |
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| 282 | v-0-8-2, 2009-08-17, r8738 |
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| 283 | ------------------------------------------------------------------- |
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| 284 | - Priorities on check results of checker |
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| 285 | - Distinguishing between errors and warnings in checker |
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| 286 | - Some on-the-fly-checks for dynamic modeling |
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| 287 | - Copy/paste support in editor |
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| 288 | - De-modularization support (elevation of a modules content to current level) |
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| 289 | variables and equations (math), places and transitions (events) not elevated |
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| 290 | - Flipping of nodes in editor for logical models |
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| 291 | - Refresh-action in editor |
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| 292 | - Status bar in editor showing status of the editor and checker |
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| 293 | - Initial support for synthetic biology by scripts generating mdl |
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| 294 | - Property to mark exportable models |
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| 295 | - Setting modules to be ignored in export (logical modeling) |
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| 296 | - Variable for map-number and monotony in logical library and editable in the GUI |
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| 297 | - Check of corresponding equation-system for a module, visualization of |
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| 298 | under- and/or overdetermined parts in incidence matrix or visual editor |
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| 299 | - Improved visual scenario editor in explorer |
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| 300 | - Improved support for workflow CellNetAnalyzer |
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| 301 | - Warning for unsaved changes on exit |
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| 302 | - Command for creation of new models |
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| 303 | - Reduced clutter in menus and toolbars |
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| 304 | - Dialogs and control panels reworked for clarity and utility |
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| 305 | - New ProMoT logo |
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| 306 | - Documentation updates |
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| 307 | |
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| 308 | ------------------------------------------------------------------- |
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| 309 | v-0-8-3, 2010-08-31, linux: r9285, win: r9303 |
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| 310 | ------------------------------------------------------------------- |
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| 311 | New Features |
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| 312 | - Option for direct loading of libraries for logical and dynamic modeling |
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| 313 | - Start simulation with Diana from ProMoT GUI |
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| 314 | - Parametrize model with Diana |
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| 315 | - Comparison of models and visualization of comparison results |
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| 316 | - Layout algorithm to visually flatten the model in Visual Explorer |
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| 317 | - Logical model of EGF receptor signaling added to knowledge base |
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| 318 | |
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| 319 | Improvements |
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| 320 | - Update libraries for logical and dynamic modeling (directions, SBO terms) |
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| 321 | - Scripts for conversion of models to updated libraries |
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| 322 | - Refactoring of rename of terminals in Visual Editor |
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| 323 | - Recalculation of terminal positions after changing canvas size in Visual Editor |
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| 324 | - Create links of submodules automatically by names in Visual Editor |
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| 325 | - Set the map number to a selection of nodes (only logical modeling) |
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| 326 | - Warning of redefinition of classes |
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| 327 | - Import/export of node/edge attribute files in Visual Explorer |
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| 328 | - Hierarchy Zoom for edges, Zoom along edge |
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| 329 | - FishEye Zoom considers edge handle points |
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| 330 | - Flexible handling of visibility of node/edge labels in Visual Explorer |
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| 331 | - Extend node size to label text in Visual Explorer |
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| 332 | - Improved scenario 'Logical Network' |
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| 333 | - Visualization of submodules with/without terminals |
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| 334 | - Export network to yEd format |
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| 335 | - Improved exception handling in ProMoT |
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| 336 | - Documentation updates |
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| 337 | |
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| 338 | Bugfixes |
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| 339 | - SBML import/export (import events, reversible flag, compartment handling) |
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| 340 | - Stability issues of Visual Explorer |
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| 341 | - Correct rendering of edge arrows in Visual Explorer |
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| 342 | - Update view after attribute file is imported in Visual Explorer |
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| 343 | |
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| 344 | ------------------------------------------------------------------- |
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| 345 | v-0-8-4, 2011-08-21, r9456 |
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| 346 | ------------------------------------------------------------------- |
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| 347 | New Features |
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| 348 | - ACL 8.2 is now used |
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| 349 | - New global scenario 'Hierarchical Level' for visualization |
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| 350 | |
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| 351 | Improvements |
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| 352 | - New build procedure and ProMoT is now installed under \usr\local\promot |
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| 353 | instead of \usr\local\diana\promot |
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| 354 | - Update Piccolo2d to version 1.3.1 |
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| 355 | - Documentation updates |
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| 356 | - Extend model statistics report in explorer: |
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| 357 | Edges with TimeScale > 1, Edges with LogicalExcluded = 1 |
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| 358 | - reduced-library.mdl: special concentration module with |
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| 359 | additional variable (conc-sink-var) |
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| 360 | |
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| 361 | Bugfixes |
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| 362 | - Corrected paths of some mdl files in the knowledge base |
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| 363 | - Corrected 'Create link' dialog |
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| 364 | (automatic connection of terminals on submodules) |
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| 365 | |
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| 366 | ------------------------------------------------------------------- |
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| 367 | v-0-8-5, 2012-0?-??, r???? |
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| 368 | ------------------------------------------------------------------- |
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| 369 | New Features |
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| 370 | - ACL 9.0 is now used |
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| 371 | - Support of the Process-Interaction-Model concept |
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| 372 | by the Process-Interaction-Library and model specialized model converters |
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| 373 | (export of rule-based models in BNGL from a PIM, |
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| 374 | conversion of PIMs to site-specific logical models) |
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| 375 | documented in a new tutorial |
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| 376 | - Extended Visual Scenarios: add options for layout and exploration schemes |
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| 377 | |
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| 378 | Improvements |
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| 379 | - Menu item, tooltips and shortcuts are added and more consistent |
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| 380 | |
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| 381 | Bugfixes |
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| 382 | - to be announced |
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