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		<id>https://wiki.biouml.org/index.php?action=history&amp;feed=atom&amp;title=PharmML</id>
		<title>PharmML - Revision history</title>
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		<updated>2026-04-24T23:10:38Z</updated>
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	<entry>
		<id>https://wiki.biouml.org/index.php?title=PharmML&amp;diff=5605&amp;oldid=prev</id>
		<title>Fkolpakov@gmail.com at 16:56, 11 February 2014</title>
		<link rel="alternate" type="text/html" href="https://wiki.biouml.org/index.php?title=PharmML&amp;diff=5605&amp;oldid=prev"/>
				<updated>2014-02-11T16:56:16Z</updated>
		
		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table class='diff diff-contentalign-left'&gt;
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			&lt;td colspan='2' style=&quot;background-color: white; color:black;&quot;&gt;← Older revision&lt;/td&gt;
			&lt;td colspan='2' style=&quot;background-color: white; color:black;&quot;&gt;Revision as of 16:56, 11 February 2014&lt;/td&gt;
			&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 1:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 1:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;PharmML - Pharmacometrics Markup Language - is a new standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;PharmML - Pharmacometrics Markup Language - is a new standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;background: #ffa; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;http://pharmml.org/&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/ins&gt;http://pharmml.org/&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;background: #ffa; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;http://ddmore.eu/pharmml&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*&lt;/ins&gt;http://ddmore.eu/pharmml&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;It was developed by&amp;#160; [[DDMoRe consortium]].&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;It was developed by&amp;#160; [[DDMoRe consortium]].&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;color: red; font-weight: bold; text-decoration: none;&quot;&gt;&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;The current version supports non-linear mixed effect models as used in analysis of continuous longitudinal population PK/PD data with:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;The current version supports non-linear mixed effect models as used in analysis of continuous longitudinal population PK/PD data with:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 17:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 18:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;**encoding of experimental data needed for typical simulation or estimation tasks, such as dosing, observations and covariates.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;**encoding of experimental data needed for typical simulation or estimation tasks, such as dosing, observations and covariates.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;*Typical modelling steps such as estimation or simulation.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;*Typical modelling steps such as estimation or simulation.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;background: #ffa; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;del class=&quot;diffchange diffchange-inline&quot;&gt; &lt;/del&gt;&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;==libPharmML==&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;There is special Java library libPharmML that provides a convenient way to read and write PharmML. It also provides basic schema based validation.&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*https://sites.google.com/site/pharmmltemp/libpharmml&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;The project is hosted on SourceForge:&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;*http://sourceforge.net/p/ddmore/pharmml/libPharmML/&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;The API should hopefully be intuitive. It can read a PharmML document,&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;write a DOM to a PharmML document, create a stub DOM and validate a DOM.&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;The PharmML DOM is generated using JAXB (see https://jaxb.java.net/)&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;to convert the XML Schema into a set of Java classes. Each schema maps&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;to a separate java package. &lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;Currently the library only validates against the XML Schema&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;definition. Addition rules such as type checking, checking for&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;duplicate symbols or dangling symbol references are not yet&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;checked.&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt;&amp;#160;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;background: #cfc; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;&amp;#160;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;[[Category:Systems pharmacology]]&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;&amp;#160;&lt;/td&gt;&lt;td style=&quot;background: #eee; color:black; font-size: smaller;&quot;&gt;&lt;div&gt;[[Category:Systems pharmacology]]&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Fkolpakov@gmail.com</name></author>	</entry>

	<entry>
		<id>https://wiki.biouml.org/index.php?title=PharmML&amp;diff=5604&amp;oldid=prev</id>
		<title>Fkolpakov@gmail.com: Created page with &quot;PharmML - Pharmacometrics Markup Language - is a new standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.  http://pharmml.org/ ht...&quot;</title>
		<link rel="alternate" type="text/html" href="https://wiki.biouml.org/index.php?title=PharmML&amp;diff=5604&amp;oldid=prev"/>
				<updated>2014-02-11T16:46:26Z</updated>
		
		<summary type="html">&lt;p&gt;Created page with &amp;quot;PharmML - Pharmacometrics Markup Language - is a new standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.  http://pharmml.org/ ht...&amp;quot;&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;PharmML - Pharmacometrics Markup Language - is a new standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.&lt;br /&gt;
&lt;br /&gt;
http://pharmml.org/&lt;br /&gt;
http://ddmore.eu/pharmml&lt;br /&gt;
&lt;br /&gt;
It was developed by  [[DDMoRe consortium]].&lt;br /&gt;
&lt;br /&gt;
The current version supports non-linear mixed effect models as used in analysis of continuous longitudinal population PK/PD data with:&lt;br /&gt;
&lt;br /&gt;
*A structural model defined as a system of ordinary differential equation (ODE) and/or algebraic equations.&lt;br /&gt;
*A flexible parameter model allowing for implementation of virtually any parameter type used in the majority of models.&lt;br /&gt;
*Discrete or continuous covariates.&lt;br /&gt;
*A nested hierarchical variability model capable of expressing very complex random error structures.&lt;br /&gt;
*An observation model with flexible residual error model supporting untransformed or transformed data.&lt;br /&gt;
*A novel trial design model allowing for &lt;br /&gt;
**definition of many common design and drug administration types &lt;br /&gt;
**encoding of experimental data needed for typical simulation or estimation tasks, such as dosing, observations and covariates.&lt;br /&gt;
*Typical modelling steps such as estimation or simulation.&lt;br /&gt;
 &lt;br /&gt;
[[Category:Systems pharmacology]]&lt;/div&gt;</summary>
		<author><name>Fkolpakov@gmail.com</name></author>	</entry>

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