From macampbell at davidson.edu Tue Jul 1 08:36:27 2014 From: macampbell at davidson.edu (Campbell, Malcolm - Faculty) Date: Tue, 1 Jul 2014 12:36:27 +0000 Subject: [Molvis-list] Running old Jmol tutorials (unsigned applets) In-Reply-To: <201406221757.s5MHvgUn021881@marlin.bio.umass.edu> References: <201406221757.s5MHvgUn021881@marlin.bio.umass.edu> Message-ID: Eric, When I use FirstGlance, is there a way to click a button to get the biological unit to show up? http://bioinformatics.org/firstglance/fgij//fg.htm?mol=3B8E&NOJAVA This is the sodium pump which many students study, but the biological unit is not what shows up. Thanks, Malcolm On Jun 22, 2014, at 1:57 PM, Eric Martz wrote: > At http://proteopedia.org/w/Installing_and_enabling_Java > > I have added instructions (at the end) for enabling Java to display unsigned Java applets. Its great that we can still do this for all those legacy Jmol tutorials that are still out there! > > You can find links to many of these tutorials at http://molviz.org > > If you find these instructions to be incomplete or confusing, please let me know! > > Eric > _______________________________________________ > Molvis-list mailing list > Molvis-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/molvis-list ________________________________________________________ A. Malcolm Campbell, Ph.D. Professor of Biology Director, James G. Martin Genomics Program Davidson College Founding Director of GCAT (www.bio.davidson.edu/GCAT ) Box 7118 (US Mail) 209 Ridge Road (shipping) Davidson, NC 28035 704-894-2692 (phone) 704-894-2512 (fax) www.bio.davidson.edu/campbell From emartz at microbio.umass.edu Thu Jul 3 15:50:56 2014 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 03 Jul 2014 15:50:56 -0400 Subject: [Molvis-list] Running old Jmol tutorials (unsigned applets) In-Reply-To: References: <201406221757.s5MHvgUn021881@marlin.bio.umass.edu> Message-ID: <201407031951.s63Jp1M4009203@marlin.bio.umass.edu> Hi, Malcolm, Well it won't hurt for the entire list to be aware of this. In the initial control panel ("molecule information", tab labeled with the PDB code), below the section on Asymmetric Unit, there is a link Biological Unit. Yes, viewing it is only a few clicks away. There is also a link for getting the Biological Unit under the Resources tab. It is always best to check the Biological Unit for every structure in order to be aware of how it may differ from the Asymmetric Unit published by crystallographers. Those terms are defined/explained in the help within FirstGlance in Jmol, and further via links within FirstGlance in Jmol. In the case of 3b8e, the biological unit is half of the asymmetric unit, namely it is a 3-chain trimer (instead of two copies, six chains). Regards, Eric At 7/1/14, you wrote: >Eric, >When I use FirstGlance, is there a way to click a button to get the >biological unit to show up? > >http://bioinformatics.org/firstglance/fgij//fg.htm?mol=3B8E&NOJAVA > >This is the sodium pump which many students study, but the >biological unit is not what shows up. > >Thanks, >Malcolm > > > > >On Jun 22, 2014, at 1:57 PM, Eric Martz wrote: > > > At http://proteopedia.org/w/Installing_and_enabling_Java > > > > I have added instructions (at the end) for enabling Java to > display unsigned Java applets. Its great that we can still do this > for all those legacy Jmol tutorials that are still out there! > > > > You can find links to many of these tutorials at http://molviz.org > > > > If you find these instructions to be incomplete or confusing, > please let me know! > > > > Eric > > _______________________________________________ > > Molvis-list mailing list > > Molvis-list at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/molvis-list > >________________________________________________________ >A. Malcolm Campbell, Ph.D. >Professor of Biology >Director, James G. Martin Genomics Program >Davidson College >Founding Director of GCAT (www.bio.davidson.edu/GCAT ) > >Box 7118 (US Mail) >209 Ridge Road (shipping) >Davidson, NC 28035 >704-894-2692 (phone) >704-894-2512 (fax) >www.bio.davidson.edu/campbell > > > > > >_______________________________________________ >Molvis-list mailing list >Molvis-list at bioinformatics.org >http://www.bioinformatics.org/mailman/listinfo/molvis-list From asidhu at biomap.org Wed Jul 16 20:51:30 2014 From: asidhu at biomap.org (Amandeep Sidhu) Date: Thu, 17 Jul 2014 08:51:30 +0800 Subject: [Molvis-list] CFP: International Journal of Semantic and Infrastructure Services Message-ID: Call for Regular Papers: International Journal of Semantic and Infrastructure Services http://www.inderscience.com/jhome.php?jcode=ijsis ISSN online: 2051-5081 ISSN print: 2051-5073 The goal of IJSIS is to propose novel semantic approaches and technologies and demonstrate how these help in improving big data management. It aims to establish an effective channel of communication between policy makers, government agencies, academic research institutions and persons concerned with the complex role of data infrastructure in society. It also intends to promote and coordinate developments in the field of semantic web and how these improve data and information infrastructure. The international dimension is emphasised in order to address the diversity of data and information that spreads across national barriers and to meet the needs of accelerating technological changes in a global economy. IJSIS provides a vehicle to help professionals, academics, researchers and policy makers, working in the field of data management, semantic web and computing infrastructure, to disseminate information and to learn from each other's work. The intended audiences are data mining researchers/practitioners; specialists in academia and industry; experts who rely on computer tools for data integration, data management, data analysis; mathematicians/statisticians who are interested in model development and simulation for data; computer scientists; and post-graduate students with interests in developing and/or applying novel algorithms/methods in large-scale data management in any domain. IJSIS publishes original papers, review papers, case studies, conference reports and book reviews. Special Issues devoted to important topics in semantics and infrastructure technology management will occasionally be published. Topics covered include ? Big data and its management ? Data integration and interoperability ? Semantic web technologies and formalisms for data ? Language processing techniques/principles for building/maintaining ontologies ? Scientific workflows and data cloud ? Semantic image analysis ? Ontologies and semantic web tools ? Ontology representation and exchange languages ? Ontology-assisted extraction and information retrieval from text collections ? Web 2.0 and Web 3.0 applications ? Novel architectural models for high performance and cloud computing ? New parallel/concurrent programming models for high performance applications ? Data security, privacy and jurisdiction of applications in the cloud ? Interoperability between different utility computing platforms ? Semantics in platforms and software as a service Paper Submission Guidelines ? All articles for this journal must be submitted using our online submissions system. Read our Submitting articles page ( http://www.inderscience.com/info/inauthors/author_submit.php). You need to register to use our online submission system. This is a one-time process. Choose "Int. Journal of Semantic and Infrastructure Services" in the dropdown list. ? 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Editor in Chief Sidhu, Amandeep S., Curtin University, Sarawak, Malaysia (ijsis at biomap.org) Associate Editors Dhillon, Sarinder K., University of Malaya, Malaysia McGregor, Carolyn, University of Ontario Institute of Technology, Canada Wang, Jason T.L., New Jersey Institute of Technology, USA Editorial Board Members Bansal, Srividya Kona, Arizona State University at the Polytechnic Campus, USA Batini, Carlo, University of Milano?Bicocca, Italy Bhowmik, Rajdeep, Cisco Systems, Inc., USA Byna, Suren, Lawrence Berkeley National Laboratory, USA Ceravolo, Paolo, Universit? degli Studi di Milano, Italy Ciuciu, Ioana, Vrije Universiteit Brussel, Belgium Ferber, Marvin, University of Bayreuth, Germany Hong, Wei-Chiang Samuelson, Oriental Institute of Technology, Taiwan Jarrar, Mustafa, Birzeit University, Palestinian Territory, Occupied Ko, Ryan, University of Waikato, New Zealand Li, Wei, University of Sydney, Australia Lukose, Dickson, MIMOS Berhad, Malaysia Panahizar, Maryam, Wright State University, USA Qian, Weining, East China Normal University, China Rajaraman, Kanagasabai, Institute for Infocomm Research (I2R), Singapore Roche, Christophe, Universit? de Savoie, France Sahoo, Satya, Case Western Reserve University, USA Sakharkar, Meena Kishore, University of Tsukuba, Japan Serafini, Luciano, Fondazione Bruno Kessler, Italy Town, Christopher, University of Cambridge, UK From emartz at microbio.umass.edu Sat Jul 26 20:05:37 2014 From: emartz at microbio.umass.edu (Eric Martz) Date: Sat, 26 Jul 2014 20:05:37 -0400 Subject: [Molvis-list] Windows 7 Fix for Jmol with Java 7 Update 65 Message-ID: <201407270005.s6R05m6D024632@marlin.bio.umass.edu> After updating Java 7 to update 65 (the current update) we have seen several Windows 7 systems where the Jmol java applet stopped working. The Jmol area remains blank and Java fails to start. There are no error messages. Not every Windows 7 system did this. If you experience this problem, I have explained two possible fixes here: http://proteopedia.org/wiki/index.php/Installing_and_enabling_Java#Windows The problem appears to be a bug in Oracle's update installer, which fails to remove some traces of the previous version. We have seen no problems in OS X or Windows XP. This problem affects only the use of Jmol_S (signed Jmol applet, e.g. one option in FirstGlance in Jmol) or older websites that still use the unsigned Jmol Java applet. The problem has no effect on JSmol, which does not require Java. (Confused? See 'Jmol Has Four Forms', http://proteopedia.org/wiki/index.php/Jmol#Jmol_Has_Four_Forms) Sincerely, Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance: 3D Views in Nature - http://firstglance.jmol.org 3D Protein Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Interactive Molecules in Public Spaces http://MolecularPlayground.Org Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ From emartz at microbio.umass.edu Wed Aug 6 10:59:03 2014 From: emartz at microbio.umass.edu (Eric Martz) Date: Wed, 06 Aug 2014 10:59:03 -0400 Subject: [Molvis-list] MolviZ.Org Updated Message-ID: <53E242B7.80600@microbio.umass.edu> MolviZ.Org has been thoroughly and systematically upgraded, and also Top5.MolviZ.Org . Many of the tutorials there are now available in JSmol (no Java needed), including the tutorial on DNA double helix structure (thanks to ?ngel Herr?ez!). Those are now clearly marked *JSmol*, and will work on recent iPads and some smart phones. For those tutorials still using the old unsigned Jmol Java applet (now marked *Jmol*), step-by-step instructions have been provided for installing and enabling Java , in both Windows and OS X, for the five most popular web browsers. You are now directed to those instructions before you get to the actual tutorial. Also for a long time now, both Proteopedia.Org and FirstGlance.Jmol.Org default to JSmol (no Java), but each has an option to use Java if desired. There are many excellent tutorials on specific molecules in Proteopedia.Org. Resources that utilize FirstGlance consequently also work in JSmol (no Java), such as the journal /Nature/ (among others ), evolutionary conservation at ConSurf, functional protein assemblies/biological units (MakeMultimer server), lipid bilayer boundaries for integral membrane proteins (Orientations of Proteins in Membranes server), and the Atlas of Macromolecules (Atlas.MolviZ.Org ). All of these are available in the /Resources/ tab within FirstGlance.Jmol.Org (except the Atlas). Thanks to Bob Hanson for his brilliant and tireless efforts that have made JSmol an amazing reality! Eric -- Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- Martz.MolviZ.Org * Top Five 3D MolVis Tools: Top5.MolviZ.Org * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org * Protein 3D Structure Wiki: Proteopedia.Org * Education: Biochem in 3D at MolviZ.Org * Find Functional Patches in Proteins: ConSurf * Atlas of Macromolecules: Atlas.MolviZ.Org * Interactive Molecules in Architectural Spaces: MolecularPlayground.Org * Workshops: Workshops.MolviZ.Org