Differences

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--- start [21:57 12.09.2017] – Walter
+++ start [12:38 20.02.2023] (current) – Jörn Starruß
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 Morpheus is a modeling and simulation environment for the study of multiscale and multicellular systems.
-Morpheus is being developed by Jörn Starruß and [[http://walter.deback.net|Walter de Back]] at the [[http://imc.zih.tu-dresden.de/imc|IMC group]] headed by prof. [[http://imc.zih.tu-dresden.de/imc/index.php?page=members&who=deutsch|Andreas Deutsch]]. We are part of the [[http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih|Center for High Performance Computing]] and the [[https://tu-dresden.de/med/mf/imb?set_language=en|Institute for Medical Informatics and Biometry]] at the [[http://www.tu-dresden.de/en|TU Dresden]], Germany.
+Morpheus is being developed by [[https://tu-dresden.de/zih/die-einrichtung/struktur/joern-starruss|Jörn Starruß]], [[http://walter.deback.net|Walter de Back]] and [[https://www.digs-bb.de/research/research-groups/lutz-brusch|Lutz Brusch]] at the [[http://imc.zih.tu-dresden.de/imc|IMC group]] headed by Prof. [[http://imc.zih.tu-dresden.de/imc/index.php?page=members&who=deutsch|Andreas Deutsch]]. We are part of the [[http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih|Center for High Performance Computing]] and the [[https://tu-dresden.de/med/mf/imb?set_language=en|Institute for Medical Informatics and Biometry]] at the [[http://www.tu-dresden.de/en|TU Dresden]], Germany.
-^  Morpheus Workshop at Multiscale Biology Summer school, Nottingham <sup>September 2017</sup>  ^^
+^  Website moved -- <sup>Jan 2019</sup>  ^^
-| {{https://upload.wikimedia.org/wikipedia/commons/thumb/9/90/Council-House-Nottingham.jpg/1920px-Council-House-Nottingham.jpg?direct&100 }} We are excited to present Morpheus in a practical session at the [[http://www.multiscalebiology.org.uk/events/event/multiscale-biology-summer-school/|Multiscale Biology Summer school]] organized by prof. Markus Owen from the UK Multi-scale biology networks. Our session will take place on 13 September 14:30 - 17:30. \\ **Participants: please find the materials for the workshop in this [[https://gitlab.com/wdeback/Workshop-Morpheus-Nottingham|GitLab repo]]**.||
+| {{:logo.png?100 |}} **<color #ad1c24>We moved our website</color> to a new [[https://morpheus.gitlab.io | location]]**. \\ Most information here is still valid, but for current releases, blogs and tutorials read  [[https://morpheus.gitlab.io]]||
-^  Updated the Windows binaries <sup>June 2017</sup>  ^^
-| After we were [[https://twitter.com/margrietpalm/status/875257377615994880|made aware]] that the binary package for MS Windows were outdated, we have now built and uploaded the Windows packages. They now reflect the current [[https://gitlab.com/morpheus.lab/morpheus|master branch]]. Please find the new version on the [[https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=download:download|download page]]. ||
-^  Talk and workshop at Institute for Computational Biology in Munich <sup>May 2017</sup>  ^^
-| On Tuesday May 30, 2017, Walter de Back will present Morpheus at the [[https://www.helmholtz-muenchen.de/icb/institute/|Institute for Computational Biology, Helmholtz Zentrum München]], hosted by [[https://www.helmholtz-muenchen.de/icb/institute/staff/staff/ma/2519/Dr.-Ing.-Hasenauer/index.html|Jan Hasenauer]]. After the lecture, there will be room for a hands-on session. If you want to join this session, please [[https://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=download:download|download and install Morpheus]] in advance. ||
-^  Workshop at Helmholtz Centre for Infection Research in Braunschweig <sup>May 2017</sup>  ^^
-| As part of a graduate school workshop on Systems Biology at the [[https://www.helmholtz-hzi.de/en/|HZI in Braunschweig]], we gave a one-day workshop on multi-scale modeling of multicellular systems. Some 15 PhD students and postdocs with various backgrounds were introduced to Morpheus with a lecture, tutorial and a hands-on session. {{https://pbs.twimg.com/media/C--wxmBXgAErdkp.jpg?direct&300 }} {{ https://pbs.twimg.com/media/C--0yb4XsAAzb8t.jpg?direct&300}} ||
-^  Summer school on Math Biol of Tissue Mechanics in Leiden <sup>June 2016</sup>  ^^
-| At the [[https://www.lorentzcenter.nl/lc/web/2016/803/info.php3?wsid=803|ESMTB/EMS summer school on tissue mechanics]], 40 young researchers from all over the world gathered at the Lorentz center in Leiden, the Netherlands, for a hands-on workshop mathematical approaches to analyze and model the biomechanics of tissues and the collective behavior of cells. Our team used Morpheus to investigate the effects of feedback between tissue packing and planar cell polarity (PCP).  {{https://pbs.twimg.com/media/Cows5qYW8AA6H1A.jpg?direct&300 }}{{ https://pbs.twimg.com/media/CpBbR6IWAAAyGIP.jpg?direct&300}} ||
-^  Morpheus in Current Opinion in Biotechnology review <sup>May 2016</sup>  ^^
-| A recent review in Current Opinion in Biotechnology on multi-class and multi-scale models of complex biological phenomena mentions Morpheus: "//...software tools, most recently Morpheus and Smoldyn [...], have been developed to allow a broader audience to access this framework.// ". See the [[[[documentation:publications|publication page]] or read the [[http://dx.doi.org/10.1016/j.copbio.2016.04.002|paper]]. ||
-^  Beta version of Morpheus 2.0 released <sup>March 2016</sup>  ^^
-| [[:download:whatsnew|{{:logo.png?direct&64 |}}]] We are proud to announce the release of a //beta version// of the new Morpheus 2.0! This release provides a [[download:whatsnew|wide range of new features]] to make modeling more flexible and the graphical interface more intuitive. Importantly, it is released under an //open source license// on our new [[https://gitlab.com/morpheus.lab/morpheus|GitLab repository]]. This provides transparency and extensibility by allowing users to develop their customized plugins. We are aiming to create a //community of developers// around Morpheus 2.0 and are looking forward to your contributions! Curious? Have a look at the [[download:whatsnew|"what's new"]] page, [[download:download|download]] the binary package, or check out the [[https://gitlab.com/morpheus.lab/morpheus|source repository]]. \\ <sub>Please note that this is a beta release: it is feature-complete but can contain bugs and is not advised for production work.</sub> ||
-^  Morpheus Courses and Workshops <sup>November 2015</sup>  ^^
-| Lots of Morpheus events this month! Besides the [[http://walter.deback.net/thesis|thesis defense]] by Walter de Back, we did a workshop for [[http://tu-dresden.de/die_tu_dresden/fakultaeten/medizinische_fakultaet/inst/imb|IMB, TU Dresden]] and [[http://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/overview/index.html|ICB, Helmholtz München]], a [[http://www.dresden-ipp.de/research/research-groups/lutz-brusch/|course on tissue patterning]] for the Dresden Graduate School for Biomedicine and Bioengineering ([[http://www.dresden-ipp.de/partners/digs-bb/|DIGS-BB]]) and a workshop for the [[https://sysbioiflysib.wordpress.com/|SysBio group at UNLP]] in Argentina (see the [[https://sysbioiflysib.wordpress.com/news/hands-on-morpheus-workshop/|pictures]]). And there is more to come. [[http://walter.deback.net/contact/|Contact us]] if you are interested in joining or organizing a workshop. ||
-^  Open source release coming soon! <sup>April 2015</sup>  ^^
-| We are currently preparing a major new release of Morpheus, version 2.0! This release adds transparency, customizability and extensibility. The source code will be distributed under open source license. Morpheus 2 includes a stable API to enable plugin development. We redesigned MorpheusML to improve modeling flexibility and its consistency with formats such as SBML. We further improved the in-code and in-app documentation. We can't wait to release and share the code with you. \\ **Check out [[download:whatsnew|the new features]].** ||
-^  Morpheus version 1.2 released! <sup>Nov 2014</sup>  ^^
-| [[:download:whatsnew|{{:download:preview_morpheus1.png?direct&160 |}}]] We are happy to announce the release of a brand new version of Morpheus! Version 1.2 improves modeling flexibility, automatic scheduling and computational efficiency. It features a new preview panel and we added three new [[examples:examples|example models]] showing new features. **Check out [[download:whatsnew|what is new]] or  [[download:download|download Morpheus 1.2]] directly.** ||
-^  Workshop on Computational Stem Cell Biology <sup>Oct 2014</sup>  ^^
-| {{:gscn.png?direct&160 |}} The [[http://www.gscn.org|German Stem Cell Network]] organized a [[http://tu-dresden.de/die_tu_dresden/fakultaeten/medizinische_fakultaet/inst/imb/folder_events/gscn2014|workshop on Computational Stem Cell Biology]] in Dresden, 1-2 December 2014. Morpheus was used in a hands-on session to construct multicellular and multiscale models. [[http://tu-dresden.de/die_tu_dresden/fakultaeten/medizinische_fakultaet/inst/imb/folder_events/gscn2014|More info]]||
-^  Morpheus User Forum <sup>Jul 2014</sup>  ^^
-| We have opened a new [[forum:users|forum]] for questions from users. Please use this forum for modeling issues, implementation questions, bug reports and feature requests. To post a question, visit the [[forum:users|Morpheus user forum]] or mail it to: <morpheus-users@googlegroups.com>||
-<sup>[[:announcements|Previous announcements]]</sup>
 {{ vimeo>70842450?large }}
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 Morpheus implements algorithms and solvers for the simulation and integration of cell-based (Potts) models, reaction-diffusion systems and models of ordinary differential equations. Due to its modular design, it allows a range of auxiliary spatiotemporal models to be constructed.
-Check out the [[examples:examples|example models]] for an overview of modeling possibilities. For details, see the [[documentation:manual|user manual]].
+Check out the [[https://morpheus.gitlab.io/#examples|example models]] for an overview of modeling possibilities. For details, see the [[documentation:manual|user manual]].
 ==== Modeling without programming ====
@@ Line 64: / Line 41: @@
 ==== Publications ====
-Check out the list of [[documentation:publications|publications]] for papers on Morpheus or its application in research and education.
+Check out the list of [[https://morpheus.gitlab.io/#publications|publications]] for papers on Morpheus or its application in research and education.
@@ Line 79: / Line 56: @@
 // Μορφευς is the Greek god of dreams. The name signifies the fashioner or moulder, because he shaped or formed the dreams which appeared to the sleeper. (Ovid's Metamorphoses xi. 635., [[http://www.perseus.tufts.edu/hopper/text?doc=Perseus%3Atext%3A1999.04.0104%3Aalphabetic+letter%3DM%3Aentry+group%3D29%3Aentry%3Dmorpheus-bio-1|Smith, 1873]]). //