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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"><channel><title>Activity for Kinetic Simulation Algorithm Ontology</title><link>https://sourceforge.net/p/kisao/activity/</link><description>Recent activity for Kinetic Simulation Algorithm Ontology</description><language>en</language><lastBuildDate>Sat, 30 Jan 2021 23:04:05 -0000</lastBuildDate><item><title>Jonathan Karr committed [r235]</title><link>https://sourceforge.net/p/kisao/code/235/</link><description>Added algorithms for iBioSim bunker and emc-sim methods, VCell finite volume methods, and VCell hybrid IDA/CVODE method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Sat, 30 Jan 2021 23:04:05 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/235/</guid></item><item><title>Jonathan Karr committed [r234]</title><link>https://sourceforge.net/p/kisao/code/234/</link><description>Added algorithm and parameter terms for iBioSim methods:</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 25 Jan 2021 20:53:10 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/234/</guid></item><item><title>Jonathan Karr committed [r233]</title><link>https://sourceforge.net/p/kisao/code/233/</link><description>Added missing subclass annotation for KISAO_0000435 of KISAO_0000302</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Tue, 19 Jan 2021 15:30:38 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/233/</guid></item><item><title>Jonathan Karr committed [r232]</title><link>https://sourceforge.net/p/kisao/code/232/</link><description>added links to BioSimulators for VCell</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 13 Jan 2021 22:52:29 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/232/</guid></item><item><title>Jonathan Karr committed [r231]</title><link>https://sourceforge.net/p/kisao/code/231/</link><description>Added algorithm and parameter terms for Salis hybrid methods implemented in VCell</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 13 Jan 2021 22:40:46 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/231/</guid></item><item><title>Jonathan Karr modified ticket #84</title><link>https://sourceforge.net/p/kisao/feature-requests/84/</link><description>Some recently added terms are not visibile in the Ontology Lookup Service</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 14 Dec 2020 19:49:21 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/84/</guid></item><item><title>Jonathan Karr posted a comment on ticket #84</title><link>https://sourceforge.net/p/kisao/feature-requests/84/?limit=25#d8ff</link><description>This appears to be fixed</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 14 Dec 2020 19:49:15 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/84/?limit=25#d8ff</guid></item><item><title>Jonathan Karr committed [r230]</title><link>https://sourceforge.net/p/kisao/code/230/</link><description>Version 2.10: Corrected capitalization of OptFlux to Optflux, Added BioSimulators identifiers for simulation tools</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Sat, 12 Dec 2020 22:57:32 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/230/</guid></item><item><title>Jonathan Karr committed [r229]</title><link>https://sourceforge.net/p/kisao/code/229/</link><description>adding directory for v2.9 files</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Fri, 20 Nov 2020 16:02:19 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/229/</guid></item><item><title>Jonathan Karr committed [r228]</title><link>https://sourceforge.net/p/kisao/code/228/</link><description>creating tag for version 2.9</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Thu, 19 Nov 2020 18:59:56 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/228/</guid></item><item><title>Jonathan Karr modified ticket #85</title><link>https://sourceforge.net/p/kisao/feature-requests/85/</link><description>New algorithm for GillesPy2 Hybrid Tau-Leaping Method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Thu, 19 Nov 2020 18:51:09 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/85/</guid></item><item><title>Jonathan Karr committed [r227]</title><link>https://sourceforge.net/p/kisao/code/227/</link><description>adding algorithms and parameters for COBRA Toolbox, Optflux, RAVEN, The Cell Collective, MaBoSS, E-Cell 4, JSim, SBSCL, BioUML, COBRApy; organizing order and tolerance parameters; fixing data types of created dates; bumping to version 2.9</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Thu, 19 Nov 2020 18:49:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/227/</guid></item><item><title>Jonathan Karr posted a comment on ticket #85</title><link>https://sourceforge.net/p/kisao/feature-requests/85/?limit=25#beaf</link><description>Will be added as KISAO_0000575</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Fri, 06 Nov 2020 22:39:03 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/85/?limit=25#beaf</guid></item><item><title>Jonathan Karr created ticket #85</title><link>https://sourceforge.net/p/kisao/feature-requests/85/</link><description>New algorithm for GillesPy2 Hybrid Tau-Leaping Method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Fri, 06 Nov 2020 22:38:55 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/85/</guid></item><item><title>Jonathan Karr modified ticket #55</title><link>https://sourceforge.net/p/kisao/feature-requests/55/</link><description>New parameter for IDAS Error control strategy </description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:39:30 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/55/</guid></item><item><title>Jonathan Karr posted a comment on ticket #55</title><link>https://sourceforge.net/p/kisao/feature-requests/55/?limit=25#c119</link><description>incorporated as KISAO_0000545</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:39:29 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/55/?limit=25#c119</guid></item><item><title>Jonathan Karr modified ticket #83</title><link>https://sourceforge.net/p/kisao/feature-requests/83/</link><description>New parameter for species transition probabilities for asynchonrous logical model simulation method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:38:53 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/83/</guid></item><item><title>Jonathan Karr posted a comment on ticket #83</title><link>https://sourceforge.net/p/kisao/feature-requests/83/?limit=25#d139</link><description>incorporated as KISAO_0000574</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:38:53 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/83/?limit=25#d139</guid></item><item><title>Jonathan Karr modified ticket #82</title><link>https://sourceforge.net/p/kisao/feature-requests/82/</link><description>New algorithm for probabilistic logical model simulation method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:38:34 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/82/</guid></item><item><title>Jonathan Karr posted a comment on ticket #82</title><link>https://sourceforge.net/p/kisao/feature-requests/82/?limit=25#7c21</link><description>incorporated as KISAO_0000573</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:38:34 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/82/?limit=25#7c21</guid></item><item><title>Jonathan Karr modified ticket #81</title><link>https://sourceforge.net/p/kisao/feature-requests/81/</link><description>New parameter for noise level</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:38:16 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/81/</guid></item><item><title>Jonathan Karr posted a comment on ticket #81</title><link>https://sourceforge.net/p/kisao/feature-requests/81/?limit=25#cd09</link><description>incorporated as KISAO_0000572</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:38:16 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/81/?limit=25#cd09</guid></item><item><title>Jonathan Karr modified ticket #80</title><link>https://sourceforge.net/p/kisao/feature-requests/80/</link><description>New parameter for absolute tolerance adjustment factor for CVODE</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:37:48 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/80/</guid></item><item><title>Jonathan Karr posted a comment on ticket #80</title><link>https://sourceforge.net/p/kisao/feature-requests/80/?limit=25#828e</link><description>incorporated as KISAO_0000571</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:37:48 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/80/?limit=25#828e</guid></item><item><title>Jonathan Karr modified ticket #79</title><link>https://sourceforge.net/p/kisao/feature-requests/79/</link><description>New parameter for auto reduce tolerances</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:37:20 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/79/</guid></item><item><title>Jonathan Karr posted a comment on ticket #79</title><link>https://sourceforge.net/p/kisao/feature-requests/79/?limit=25#806c</link><description>incorporated as KISAO_0000570</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:37:20 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/79/?limit=25#806c</guid></item><item><title>Jonathan Karr modified ticket #78</title><link>https://sourceforge.net/p/kisao/feature-requests/78/</link><description>New algorithm for Stochastic second order Runge-Kutta method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:37:01 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/78/</guid></item><item><title>Jonathan Karr posted a comment on ticket #78</title><link>https://sourceforge.net/p/kisao/feature-requests/78/?limit=25#30d7</link><description>incorporated as KISAO_0000566</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:37:01 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/78/?limit=25#30d7</guid></item><item><title>Jonathan Karr modified ticket #77</title><link>https://sourceforge.net/p/kisao/feature-requests/77/</link><description>New algorithm for nleq2</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:36:36 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/77/</guid></item><item><title>Jonathan Karr posted a comment on ticket #77</title><link>https://sourceforge.net/p/kisao/feature-requests/77/?limit=25#ea13</link><description>incorporated as KISAO_0000569</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:36:36 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/77/?limit=25#ea13</guid></item><item><title>Jonathan Karr modified ticket #76</title><link>https://sourceforge.net/p/kisao/feature-requests/76/</link><description>New algorithm for Stochastic differential equation method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:36:06 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/76/</guid></item><item><title>Jonathan Karr modified ticket #75</title><link>https://sourceforge.net/p/kisao/feature-requests/75/</link><description>New parameter for force physical correctness</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:35:51 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/75/</guid></item><item><title>Jonathan Karr posted a comment on ticket #75</title><link>https://sourceforge.net/p/kisao/feature-requests/75/?limit=25#0ba4</link><description>incorporated as KISAO_0000567</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:35:51 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/75/?limit=25#0ba4</guid></item><item><title>Jonathan Karr modified ticket #74</title><link>https://sourceforge.net/p/kisao/feature-requests/74/</link><description>New parameter for absolute tolerance for root finding</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:35:26 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/74/</guid></item><item><title>Jonathan Karr posted a comment on ticket #74</title><link>https://sourceforge.net/p/kisao/feature-requests/74/?limit=25#eefb</link><description>incorporated as KISAO_0000565</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:35:26 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/74/?limit=25#eefb</guid></item><item><title>Jonathan Karr modified ticket #73</title><link>https://sourceforge.net/p/kisao/feature-requests/73/</link><description>New algorithm for stochastic Runge-Kutta method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:34:53 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/73/</guid></item><item><title>Jonathan Karr posted a comment on ticket #73</title><link>https://sourceforge.net/p/kisao/feature-requests/73/?limit=25#aa53</link><description>incorporated as KISAO_0000564</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:34:53 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/73/?limit=25#aa53</guid></item><item><title>Jonathan Karr modified ticket #71</title><link>https://sourceforge.net/p/kisao/feature-requests/71/</link><description>New algorithm for Pahle hybrid Gibson-Bruck Next Reaction method/LSODA method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:33:57 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/71/</guid></item><item><title>Jonathan Karr posted a comment on ticket #71</title><link>https://sourceforge.net/p/kisao/feature-requests/71/?limit=25#bd82</link><description>incorporated as KISAO_0000562</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:33:57 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/71/?limit=25#bd82</guid></item><item><title>Jonathan Karr modified ticket #72</title><link>https://sourceforge.net/p/kisao/feature-requests/72/</link><description>Pahle hybrid Gibson-Bruck Next Reaction method/RK-45 method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:33:46 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/72/</guid></item><item><title>Jonathan Karr posted a comment on ticket #72</title><link>https://sourceforge.net/p/kisao/feature-requests/72/?limit=25#9a9c</link><description>incorporated as KISAO_0000563</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:33:46 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/72/?limit=25#9a9c</guid></item><item><title>Jonathan Karr modified ticket #70</title><link>https://sourceforge.net/p/kisao/feature-requests/70/</link><description>New algorithm for Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta metho</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:33:25 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/70/</guid></item><item><title>Jonathan Karr posted a comment on ticket #70</title><link>https://sourceforge.net/p/kisao/feature-requests/70/?limit=25#f6fb</link><description>incorporated as KISAO_0000561</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:33:25 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/70/?limit=25#f6fb</guid></item><item><title>Jonathan Karr modified ticket #69</title><link>https://sourceforge.net/p/kisao/feature-requests/69/</link><description>New algorithm for LSODA or LSODAR</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:32:18 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/69/</guid></item><item><title>Jonathan Karr posted a comment on ticket #69</title><link>https://sourceforge.net/p/kisao/feature-requests/69/?limit=25#e795</link><description>incorporated as KISAO_0000560</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:32:18 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/69/?limit=25#e795</guid></item><item><title>Jonathan Karr modified ticket #68</title><link>https://sourceforge.net/p/kisao/feature-requests/68/</link><description>New parameter for initial step size</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:32:02 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/68/</guid></item><item><title>Jonathan Karr posted a comment on ticket #68</title><link>https://sourceforge.net/p/kisao/feature-requests/68/?limit=25#5cd8</link><description>incorporated as KISAO_0000559</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:32:02 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/68/?limit=25#5cd8</guid></item><item><title>Jonathan Karr modified ticket #67</title><link>https://sourceforge.net/p/kisao/feature-requests/67/</link><description>Parameter for relative steady-state tolerance for CVODES</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:31:31 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/67/</guid></item><item><title>Jonathan Karr posted a comment on ticket #67</title><link>https://sourceforge.net/p/kisao/feature-requests/67/?limit=25#a611</link><description>incorporated as KISAO_0000558</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:31:30 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/67/?limit=25#a611</guid></item><item><title>Jonathan Karr modified ticket #65</title><link>https://sourceforge.net/p/kisao/feature-requests/65/</link><description>Parameter for relative quadrature tolerance for CVODES</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:31:22 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/65/</guid></item><item><title>Jonathan Karr posted a comment on ticket #65</title><link>https://sourceforge.net/p/kisao/feature-requests/65/?limit=25#9391</link><description>incorporated as KISAO_0000556</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:31:22 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/65/?limit=25#9391</guid></item><item><title>Jonathan Karr modified ticket #66</title><link>https://sourceforge.net/p/kisao/feature-requests/66/</link><description>Parameter for absolute steady-state tolerance for CVODES</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:30:56 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/66/</guid></item><item><title>Jonathan Karr posted a comment on ticket #66</title><link>https://sourceforge.net/p/kisao/feature-requests/66/?limit=25#2c83</link><description>incorporated as KISAO_0000557</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:30:56 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/66/?limit=25#2c83</guid></item><item><title>Jonathan Karr modified ticket #64</title><link>https://sourceforge.net/p/kisao/feature-requests/64/</link><description>Parameter for absolute quadrature tolerance for CVODES</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:30:46 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/64/</guid></item><item><title>Jonathan Karr posted a comment on ticket #64</title><link>https://sourceforge.net/p/kisao/feature-requests/64/?limit=25#bd37</link><description>incorporated as KISAO_0000555</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:30:46 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/64/?limit=25#bd37</guid></item><item><title>Jonathan Karr modified ticket #63</title><link>https://sourceforge.net/p/kisao/feature-requests/63/</link><description>New algorithm for parsimonious FBA (min number of active fluxes)</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:29:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/63/</guid></item><item><title>Jonathan Karr posted a comment on ticket #63</title><link>https://sourceforge.net/p/kisao/feature-requests/63/?limit=25#f665</link><description>incorporated as KISAO_0000554</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:29:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/63/?limit=25#f665</guid></item><item><title>Jonathan Karr modified ticket #62</title><link>https://sourceforge.net/p/kisao/feature-requests/62/</link><description>New algorithm for quadratic convex optimization</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:29:22 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/62/</guid></item><item><title>Jonathan Karr posted a comment on ticket #62</title><link>https://sourceforge.net/p/kisao/feature-requests/62/?limit=25#4126</link><description>incorporated as KISAO_0000548</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:29:22 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/62/?limit=25#4126</guid></item><item><title>Jonathan Karr modified ticket #61</title><link>https://sourceforge.net/p/kisao/feature-requests/61/</link><description>New algorithm for linear convex optimization</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:28:59 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/61/</guid></item><item><title>Jonathan Karr posted a comment on ticket #61</title><link>https://sourceforge.net/p/kisao/feature-requests/61/?limit=25#074c</link><description>incorporated as KISAO_0000547</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:28:59 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/61/?limit=25#074c</guid></item><item><title>Jonathan Karr modified ticket #60</title><link>https://sourceforge.net/p/kisao/feature-requests/60/</link><description>New parameter for optimization solver</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:28:35 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/60/</guid></item><item><title>Jonathan Karr posted a comment on ticket #60</title><link>https://sourceforge.net/p/kisao/feature-requests/60/?limit=25#fb3c</link><description>incorporated as KISAO_0000553</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:28:35 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/60/?limit=25#fb3c</guid></item><item><title>Jonathan Karr modified ticket #59</title><link>https://sourceforge.net/p/kisao/feature-requests/59/</link><description>New parameter for optimization method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:27:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/59/</guid></item><item><title>Jonathan Karr posted a comment on ticket #59</title><link>https://sourceforge.net/p/kisao/feature-requests/59/?limit=25#6cc1</link><description>incorporated as KISAO_0000552</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:27:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/59/?limit=25#6cc1</guid></item><item><title>Jonathan Karr modified ticket #58</title><link>https://sourceforge.net/p/kisao/feature-requests/58/</link><description>New algorithm for convex optimization</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:27:06 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/58/</guid></item><item><title>Jonathan Karr posted a comment on ticket #58</title><link>https://sourceforge.net/p/kisao/feature-requests/58/?limit=25#9b8b</link><description>incorporated as KISAO_0000546</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:27:06 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/58/?limit=25#9b8b</guid></item><item><title>Jonathan Karr modified ticket #57</title><link>https://sourceforge.net/p/kisao/feature-requests/57/</link><description>New algorithm for interior point method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:26:47 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/57/</guid></item><item><title>Jonathan Karr posted a comment on ticket #57</title><link>https://sourceforge.net/p/kisao/feature-requests/57/?limit=25#a72d</link><description>Incorporated as KISAO_0000551</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:26:47 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/57/?limit=25#a72d</guid></item><item><title>Jonathan Karr modified ticket #56</title><link>https://sourceforge.net/p/kisao/feature-requests/56/</link><description>New algorithm for simplex method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:26:29 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/56/</guid></item><item><title>Jonathan Karr posted a comment on ticket #56</title><link>https://sourceforge.net/p/kisao/feature-requests/56/?limit=25#2567</link><description>Incorporated as KISAO_0000550</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:26:29 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/56/?limit=25#2567</guid></item><item><title>Jonathan Karr modified ticket #53</title><link>https://sourceforge.net/p/kisao/feature-requests/53/</link><description>New parameter for CVODES stability limit detection flag</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:25:31 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/53/</guid></item><item><title>Jonathan Karr posted a comment on ticket #53</title><link>https://sourceforge.net/p/kisao/feature-requests/53/?limit=25#e382</link><description>Incorporated as KISAO_0000543</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:25:31 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/53/?limit=25#e382</guid></item><item><title>Jonathan Karr modified ticket #54</title><link>https://sourceforge.net/p/kisao/feature-requests/54/</link><description>New algorithm for IDAS</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:24:51 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/54/</guid></item><item><title>Jonathan Karr posted a comment on ticket #54</title><link>https://sourceforge.net/p/kisao/feature-requests/54/?limit=25#9857</link><description>incorporated as KISAO_0000544</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:24:51 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/54/?limit=25#9857</guid></item><item><title>Jonathan Karr modified ticket #52</title><link>https://sourceforge.net/p/kisao/feature-requests/52/</link><description>New parameter for VODE Jacobian</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:24:22 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/52/</guid></item><item><title>Jonathan Karr posted a comment on ticket #52</title><link>https://sourceforge.net/p/kisao/feature-requests/52/?limit=25#32b0</link><description>Incorporated as KISAO_0000542</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:24:22 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/52/?limit=25#32b0</guid></item><item><title>Jonathan Karr modified ticket #51</title><link>https://sourceforge.net/p/kisao/feature-requests/51/</link><description>New parameter for dopri5 beta</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:23:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/51/</guid></item><item><title>Jonathan Karr posted a comment on ticket #51</title><link>https://sourceforge.net/p/kisao/feature-requests/51/?limit=25#5ac8</link><description>Incorporated as KISAO_0000541</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:23:50 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/51/?limit=25#5ac8</guid></item><item><title>Jonathan Karr modified ticket #49</title><link>https://sourceforge.net/p/kisao/feature-requests/49/</link><description>New parameter for dopri5 dfactor</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:23:31 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/49/</guid></item><item><title>Jonathan Karr posted a comment on ticket #49</title><link>https://sourceforge.net/p/kisao/feature-requests/49/?limit=25#05ec</link><description>Incorporated as KISAO_0000539</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:23:31 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/49/?limit=25#05ec</guid></item><item><title>Jonathan Karr modified ticket #50</title><link>https://sourceforge.net/p/kisao/feature-requests/50/</link><description>New parameter for dopri5 ifactor</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:22:54 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/50/</guid></item><item><title>Jonathan Karr posted a comment on ticket #50</title><link>https://sourceforge.net/p/kisao/feature-requests/50/?limit=25#092b</link><description>Incorporated as KISAO_0000540</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:22:54 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/50/?limit=25#092b</guid></item><item><title>Jonathan Karr modified ticket #48</title><link>https://sourceforge.net/p/kisao/feature-requests/48/</link><description>New parameter for dopri5 safety</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:22:21 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/48/</guid></item><item><title>Jonathan Karr posted a comment on ticket #48</title><link>https://sourceforge.net/p/kisao/feature-requests/48/?limit=25#4869</link><description>Incorporated as KISAO_0000538</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:22:21 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/48/?limit=25#4869</guid></item><item><title>Jonathan Karr modified ticket #47</title><link>https://sourceforge.net/p/kisao/feature-requests/47/</link><description>New algorithm for RK23</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:21:53 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/47/</guid></item><item><title>Jonathan Karr posted a comment on ticket #47</title><link>https://sourceforge.net/p/kisao/feature-requests/47/?limit=25#819a</link><description>Incorporated as KISAO_0000537</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:21:53 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/47/?limit=25#819a</guid></item><item><title>Jonathan Karr modified ticket #46</title><link>https://sourceforge.net/p/kisao/feature-requests/46/</link><description>New algorithm for ZVODE</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:21:21 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/46/</guid></item><item><title>Jonathan Karr posted a comment on ticket #46</title><link>https://sourceforge.net/p/kisao/feature-requests/46/?limit=25#699d</link><description>Incorporated as KISAO_0000491</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:21:21 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/46/?limit=25#699d</guid></item><item><title>Jonathan Karr modified ticket #45</title><link>https://sourceforge.net/p/kisao/feature-requests/45/</link><description>New algorithm for VODE</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:20:48 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/45/</guid></item><item><title>Jonathan Karr posted a comment on ticket #45</title><link>https://sourceforge.net/p/kisao/feature-requests/45/?limit=25#7fa4</link><description>Incorporated as KISAO_0000535</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Mon, 02 Nov 2020 14:20:47 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/45/?limit=25#7fa4</guid></item><item><title>Anna Zhukova committed [r226]</title><link>https://sourceforge.net/p/kisao/code/226/</link><description>Tickets 45-83 (incorporated by Jonathan)</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Anna Zhukova</dc:creator><pubDate>Mon, 02 Nov 2020 10:21:20 -0000</pubDate><guid>https://sourceforge.net/p/kisao/code/226/</guid></item><item><title>Jonathan Karr posted a comment on ticket #84</title><link>https://sourceforge.net/p/kisao/feature-requests/84/?limit=25#1de9</link><description>I filed a help ticket with OLS about this</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Thu, 29 Oct 2020 19:50:58 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/84/?limit=25#1de9</guid></item><item><title>Jonathan Karr posted a comment on ticket #76</title><link>https://sourceforge.net/p/kisao/feature-requests/76/?limit=25#692d</link><description>Not needed. This has been superseded by the use of characterisitics.</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Thu, 29 Oct 2020 18:49:39 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/76/?limit=25#692d</guid></item><item><title>Jonathan Karr created ticket #84</title><link>https://sourceforge.net/p/kisao/feature-requests/84/</link><description>Some recently added terms are not visibile in the Ontology Lookup Service</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Thu, 29 Oct 2020 16:03:18 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/84/</guid></item><item><title>Jonathan Karr created ticket #83</title><link>https://sourceforge.net/p/kisao/feature-requests/83/</link><description>New parameter for species transition probabilities for asynchonrous logical model simulation method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 28 Oct 2020 21:05:09 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/83/</guid></item><item><title>Jonathan Karr created ticket #82</title><link>https://sourceforge.net/p/kisao/feature-requests/82/</link><description>New algorithm for probabilistic logical model simulation method</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 28 Oct 2020 20:53:41 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/82/</guid></item><item><title>Jonathan Karr created ticket #81</title><link>https://sourceforge.net/p/kisao/feature-requests/81/</link><description>New parameter for noise level</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 28 Oct 2020 20:48:24 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/81/</guid></item><item><title>Jonathan Karr posted a comment on ticket #55</title><link>https://sourceforge.net/p/kisao/feature-requests/55/?limit=25#e503</link><description>Change subClassOf: KISAO_0000242, KISAO_0000243</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 28 Oct 2020 19:46:54 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/55/?limit=25#e503</guid></item><item><title>Jonathan Karr posted a comment on ticket #53</title><link>https://sourceforge.net/p/kisao/feature-requests/53/?limit=25#c4d3</link><description>Change subClassOf: KISAO_0000242, KISAO_0000243</description><dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">Jonathan Karr</dc:creator><pubDate>Wed, 28 Oct 2020 19:46:14 -0000</pubDate><guid>https://sourceforge.net/p/kisao/feature-requests/53/?limit=25#c4d3</guid></item></channel></rss>