From apico at gladstone.ucsf.edu Wed Sep 12 20:17:55 2012 From: apico at gladstone.ucsf.edu (Alexander Pico) Date: Wed, 12 Sep 2012 17:17:55 -0700 Subject: [BiO BB] Invitation - Cytoscape Workshop 2012 - San Francisco, CA - December 13-14 In-Reply-To: Message-ID: Cytoscape Workshop 2012 in San Francisco, CA, Dec 13-14 The annual Cytoscape Workshop brings together the entire Cytoscape community, including users and developers, for a series of tutorials, workshops, meetings and demos. The meeting kicks off with a public symposium on the latest developments in Network Biology. Please find program and registration details at... http://nrnb.org/cyretreat/ Cytoscape is a free, open source software platform for visualizing and analyzing complex networks and associated data.?Find out more at http://cytoscape.org Program Schedule Thursday, December 13th * Public Symposium on Network Biology Friday, December 14th * Cytoscape User and Developer Tutorials * Cytoscape Plugin and App Expo Register Now Students are free! http://cytoscape.eventbrite.com/ If you have any questions, contact Alex at apico at gladstone.ucsf.edu From daniele.gianni at gmail.com Thu Sep 13 17:54:42 2012 From: daniele.gianni at gmail.com (Daniele Gianni) Date: Thu, 13 Sep 2012 23:54:42 +0200 Subject: [BiO BB] CfP: 3rd International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim13) part of the Symposium on Theory of Modeling and Simulation SCS SpringSim 2013) In-Reply-To: References: Message-ID: ################################################################# CALL FOR PAPERS 3rd International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2013) ################################################################# April 7-10, 2013, San Diego, CA (USA) http://www.sel.uniroma2.it/Mod4Sim13 ################################################################# # Papers Due: *** November 1, 2012 *** # Accepted papers will be published in the conference proceedings # and archived in the ACM Digital Library. ################################################################# The workshop aims to bring together experts in model-based, model-driven and software engineering with experts in simulation methods and simulation practitioners, with the objective to advance the state of the art in model-driven simulation engineering. Model-driven engineering approaches provide considerable advantages to software systems engineering activities through the provision of consistent and coherent models at different abstraction levels. As these models are in a machine readable form, model-driven engineering approaches can also support the exploitation of computing capabilities for model reuse, programming code generation, and model checking, for example. The definition of a simulation model, its software implementation and its execution platform form what is known as simulation engineering. As simulation systems are mainly based on software, these systems can similarly benefit from model-driven approaches to support automatic software generation, enhance software quality, and reduce costs, development effort and time-to-market. Similarly to systems and software engineering, simulation engineering can exploit the capabilities of model-driven approaches by increasing the abstraction level in simulation model specifications and by automating the derivation of simulator code. Further advantages can be gained by using modeling languages, such as UML and SysML ? but not exclusively those. For example, modeling languages can be used for descriptive modeling (to describe the system to be simulated), for analytical modeling (to specify analytically the simulation of the same system), and for implementation modeling (to define the respective simulator). A partial list of topics of interest includes: * model-driven simulation engineering processes * requirements modeling for simulation * domain specific languages for modeling and simulation * model transformations for simulation model building * model transformations for simulation model implementation * model-driven engineering of distributed simulation systems * relationship between metamodeling standards (e.g., MOF, Ecore) and distributed simulation standards (e.g., HLA, DIS) * metamodels for simulation reuse and interoperability * model-driven technologies for different simulation paradigms (discrete event simulation, multi-agent simulation, sketch-based * simulation, etc.) * model-driven methods and tools for performance engineering of simulation systems * simulation tools for model-driven software performance engineering * model-driven technologies for simulation verification and validation * model-driven technologies for data collection and analysis * model-driven technologies for simulation visualization * Executable UML * Executable Architectures * SysML / Modelica integration * Simulation Model Portability and reuse * model-based systems verification and validation * simulation for model-based systems engineering To stimulate creativity, however, the workshop maintains a wider scope and welcomes contributions offering original perspectives on model-driven engineering of simulation systems. +++++++++++++++++++++++++++++++++++ On-Line Submissions and Publication +++++++++++++++++++++++++++++++++++ We invite paper submissions in three forms: 1. Full paper (max 8 pages), describing innovative research results. These papers are eligible for the best paper award and may be invited for an extended version in a special issue of the SCS SIMULATION journal. 2. Work-in-progress paper (max 6 pages), describing novel research ideas and promising work that have not yet been fully evaluated. 3. Short paper (max 6 pages), describing industrial and hands-on experience on any relevant area (i.e. military, government, space, etc.). All the papers must be submitted through the SCS conference management systems (http://www.softconf.com/scs/DEVS13/) and select the Mod4Sim track. The submissions must be in PDF format and conform to the SCS conference template (Word template is available at http://www.scs.org/upload/documents/templates/ConferenceSubmissionWORDTemplate.doc , guidelines are available at http://www.scs.org/PDFs/formattingkit.pdf). All the submitted papers must be original and not submitted else where. Submitted papers will be peer reviewed with respect to their quality, originality and relevance. The authors of the accepted papers must register in advance for inclusion of their paper in the conference proceedings. Authors of accepted papers will be invited to update their papers basing on the reviews, before providing the camera ready. All accepted papers will be included in the conference proceedings and archived in both the ACM Digital Library. However, **only** accepted **full papers** will be printed in hard copy. Authors may contact the organizers for expression of interest and content appropriateness at any time. +++++++++++++++ Important Dates +++++++++++++++ * Submission Deadline: November 1, 2012 * Decision to paper authors: January 10, 2013 * Camera ready due: February 5, 2013 * Conference dates: April 7-10, 2013 ++++++++++++++++++++ Organizing Committee ++++++++++++++++++++ * Andrea D'Ambrogio - University of Rome TorVergata, Italy * Daniele Gianni - European Space Agency, The Netherlands +++++++++++++++++ Program Committee +++++++++++++++++ * Steffen Becker - University of Paderborn, Germany * Paolo Bocciarelli - University of Rome TorVergata, Italy * David Chen - Univeristy of Bordeaux I, France * Cristian Englert - Serco, The Netherlands * Huascar Espinoza - European Software Institute and Tecnalia, Spain * Paul A. Fishwick - University of Florida, USA * Carlos Juiz - University of Balearic Islands, Spain * Cristiano Leorato - Rhea, The Netherlands * Steve McKeever - University of Oxford, UK * Halit Oguzt?z?n - Middle East Technical University, Turkey * Andreas Tolk - Old Dominion University, USA * Hans Vangheluwe - University of Antwerp, Belgium and McGill University, Canada * Anthony Walsh - European Space Agency, Germany * Heming Zhang - Tsinghua University, China *** Contact Information *** Andrea D'Ambrogio and Daniele Gianni (workshop co-chairs) Emails: dambro at uniroma2.it and danielegmail-mod4sim at yahoo.it From jeff at bioinformatics.org Mon Sep 24 08:10:15 2012 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 24 Sep 2012 08:10:15 -0400 Subject: [BiO BB] First course this season: Introduction to DNA and Protein Sequence Analysis Message-ID: <50604DA7.2010800@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BI101 Introduction to DNA and Protein Sequence Analysis October 1-5, 2012 Live, Online at Bioinformatics.Org http://www.bioinformatics.org/edu/AGAA -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: This course teaches the individual how to analyze DNA and protein sequences using computer software. Topics to be covered include description of sequence alignments, search, formats, and various command line tools such as BLAST, FASTA, HMMER and editing software such as Geneious, Jalview, etc. INSTRUCTOR: Shailender Nagpal SYLLABUS: The course is divided into 4 sessions, roughly 1-1.5 hours each. Homework assignments will involve running computationally intensive tools. Session 1: Fundamentals of DNA and protein alphabets, representations, patterns, structures and annotations Session 2: DNA and protein sequence alignments: local, global and multiple; demonstration of tools to perform these alignments Session 3: Sequence database searches using BLAST, FASTA and SSEARCH Session 4: Additional DNA sequence analysis applications, such as gene finding, genome annotation and assembly Lecture schedule: Monday through Thursday, 16:00-17:30 GMT (12:00-1:30 PM US EDT) REGISTRATION: http://www.bioinformatics.org/edu/AGAA FOR MORE INFORMATION: Please visit: http://www.bioinformatics.org/wiki/BI101 Or contact: edu at bioinformatics.org Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 621 8258 --