Biodynamo: a New Platform for Large-Scale Biological Simulation
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MODELLER 10.1 Manual
MODELLER A Program for Protein Structure Modeling Release 10.1, r12156 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/03/12 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
Debian Developer's Reference Version 12.0, Released on 2021-09-01
Debian Developer’s Reference Release 12.0 Developer’s Reference Team 2021-09-01 CONTENTS 1 Scope of This Document 3 2 Applying to Become a Member5 2.1 Getting started..............................................5 2.2 Debian mentors and sponsors......................................6 2.3 Registering as a Debian member.....................................6 3 Debian Developer's Duties 9 3.1 Package Maintainer's Duties.......................................9 3.1.1 Work towards the next stable release............................9 3.1.2 Maintain packages in stable .................................9 3.1.3 Manage release-critical bugs.................................. 10 3.1.4 Coordination with upstream developers............................ 10 3.2 Administrative Duties.......................................... 10 3.2.1 Maintaining your Debian information............................. 11 3.2.2 Maintaining your public key.................................. 11 3.2.3 Voting.............................................. 11 3.2.4 Going on vacation gracefully.................................. 12 3.2.5 Retiring............................................. 12 3.2.6 Returning after retirement................................... 13 4 Resources for Debian Members 15 4.1 Mailing lists............................................... 15 4.1.1 Basic rules for use....................................... 15 4.1.2 Core development mailing lists................................. 15 4.1.3 Special lists........................................... 16 4.1.4 Requesting new -
Open Source Used in Influx1.8 Influx 1.9
Open Source Used In Influx1.8 Influx 1.9 Cisco Systems, Inc. www.cisco.com Cisco has more than 200 offices worldwide. Addresses, phone numbers, and fax numbers are listed on the Cisco website at www.cisco.com/go/offices. Text Part Number: 78EE117C99-1178791953 Open Source Used In Influx1.8 Influx 1.9 1 This document contains licenses and notices for open source software used in this product. With respect to the free/open source software listed in this document, if you have any questions or wish to receive a copy of any source code to which you may be entitled under the applicable free/open source license(s) (such as the GNU Lesser/General Public License), please contact us at [email protected]. In your requests please include the following reference number 78EE117C99-1178791953 Contents 1.1 golang-protobuf-extensions v1.0.1 1.1.1 Available under license 1.2 prometheus-client v0.2.0 1.2.1 Available under license 1.3 gopkg.in-asn1-ber v1.0.0-20170511165959-379148ca0225 1.3.1 Available under license 1.4 influxdata-raft-boltdb v0.0.0-20210323121340-465fcd3eb4d8 1.4.1 Available under license 1.5 fwd v1.1.1 1.5.1 Available under license 1.6 jaeger-client-go v2.23.0+incompatible 1.6.1 Available under license 1.7 golang-genproto v0.0.0-20210122163508-8081c04a3579 1.7.1 Available under license 1.8 influxdata-roaring v0.4.13-0.20180809181101-fc520f41fab6 1.8.1 Available under license 1.9 influxdata-flux v0.113.0 1.9.1 Available under license 1.10 apache-arrow-go-arrow v0.0.0-20200923215132-ac86123a3f01 1.10.1 Available under -
MODELLER 10.0 Manual
MODELLER A Program for Protein Structure Modeling Release 10.0, r12005 Andrej Saliˇ with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Guangqiang Dong, Marc A. Martı-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-care AT salilab.org URL https://salilab.org/modeller/ 2021/01/25 ii Contents Copyright notice xxi Acknowledgments xxv 1 Introduction 1 1.1 What is Modeller?............................................. 1 1.2 Modeller bibliography....................................... .... 2 1.3 Obtainingandinstallingtheprogram. .................... 3 1.4 Bugreports...................................... ............ 4 1.5 Method for comparative protein structure modeling by Modeller ................... 5 1.6 Using Modeller forcomparativemodeling. ... 8 1.6.1 Preparinginputfiles . ............. 8 1.6.2 Running Modeller ......................................... 9 2 Automated comparative modeling with AutoModel 11 2.1 Simpleusage ..................................... ............ 11 2.2 Moreadvancedusage............................... .............. 12 2.2.1 Including water molecules, HETATM residues, and hydrogenatoms .............. 12 2.2.2 Changing the default optimization and refinement protocol ................... 14 2.2.3 Getting a very fast and approximate model . ................. 14 2.2.4 Building a model from multiple templates . .................. 15 2.2.5 Buildinganallhydrogenmodel -
Common Tools for Team Collaboration Problem: Working with a Team (Especially Remotely) Can Be Difficult
Common Tools for Team Collaboration Problem: Working with a team (especially remotely) can be difficult. ▹ Team members might have a different idea for the project ▹ Two or more team members could end up doing the same work ▹ Or a few team members have nothing to do Solutions: A combination of few tools. ▹ Communication channels ▹ Wikis ▹ Task manager ▹ Version Control ■ We’ll be going in depth with this one! Important! The tools are only as good as your team uses them. Make sure all of your team members agree on what tools to use, and train them thoroughly! Communication Channels Purpose: Communication channels provide a way to have team members remotely communicate with one another. Ideally, the channel will attempt to emulate, as closely as possible, what communication would be like if all of your team members were in the same office. Wait, why not email? ▹ No voice support ■ Text alone is not a sufficient form of communication ▹ Too slow, no obvious support for notifications ▹ Lack of flexibility in grouping people Tools: ▹ Discord ■ discordapp.com ▹ Slack ■ slack.com ▹ Riot.im ■ about.riot.im Discord: Originally used for voice-chat for gaming, Discord provides: ▹ Voice & video conferencing ▹ Text communication, separated by channels ▹ File-sharing ▹ Private communications ▹ A mobile, web, and desktop app Slack: A business-oriented text communication that also supports: ▹ Everything Discord does, plus... ▹ Threaded conversations Riot.im: A self-hosted, open-source alternative to Slack Wikis Purpose: Professionally used as a collaborative game design document, a wiki is a synchronized documentation tool that retains a thorough history of changes that occured on each page. -
Rule-Based Modeling of Biochemical Systems with Bionetgen
Rule-Based Modeling of Biochemical Systems with BioNetGen James R. Faeder1, Michael L. Blinov2, and William S. Hlavacek3 Once a model specification is processed by BNG2, Short Abstract — Rule-based modeling involves the models can be exported in one of a variety of formats, representation of molecules as structured objects and including MATLAB M-files and Systems Biology Markup molecular interactions as rules for transforming the attributes language (SBML) (3). BNG2 can also generate a network of of these objects. The approach allows systematic incorporation species and reactions for simulation using either an ODE of site-specific details about protein-protein interactions into a solver or Gillespie’s stochastic simulation algorithm (4). The model for the dynamics of a signal-transduction system, as well as other applications. The consequences of protein-protein dashed line in Fig. 1 indicates that the network generation interactions are difficult to specify and track with a and stochastic simulation engines are coupled so that for conventional modeling approach because of the large number large reaction networks species and reactions can be of protein phosphoforms and protein complexes that these generated on-the-fly as needed (5, 6). Recently, particle- interactions potentially generate. Here, we focus on how a rule- based simulation methods (7, 8) have been developed that based model is specified in the BioNetGen language (BNGL) avoid the computational costs associated with explicit and how a model specification is analyzed using the BioNetGen generation of the reachable network of species and software tool. We also discuss new developments in rule-based interactions, which can become a major bottleneck for the modeling that should enable the construction and analysis of simulation of even moderate-sized rule-based models (9). -
Tuto Documentation Release 0.1.0
Tuto Documentation Release 0.1.0 DevOps people 2020-05-09 09H16 CONTENTS 1 Documentation news 3 1.1 Documentation news 2020........................................3 1.1.1 New features of sphinx.ext.autodoc (typing) in sphinx 2.4.0 (2020-02-09)..........3 1.1.2 Hypermodern Python Chapter 5: Documentation (2020-01-29) by https://twitter.com/cjolowicz/..................................3 1.2 Documentation news 2018........................................4 1.2.1 Pratical sphinx (2018-05-12, pycon2018)...........................4 1.2.2 Markdown Descriptions on PyPI (2018-03-16)........................4 1.2.3 Bringing interactive examples to MDN.............................5 1.3 Documentation news 2017........................................5 1.3.1 Autodoc-style extraction into Sphinx for your JS project...................5 1.4 Documentation news 2016........................................5 1.4.1 La documentation linux utilise sphinx.............................5 2 Documentation Advices 7 2.1 You are what you document (Monday, May 5, 2014)..........................8 2.2 Rédaction technique...........................................8 2.2.1 Libérez vos informations de leurs silos.............................8 2.2.2 Intégrer la documentation aux processus de développement..................8 2.3 13 Things People Hate about Your Open Source Docs.........................9 2.4 Beautiful docs.............................................. 10 2.5 Designing Great API Docs (11 Jan 2012)................................ 10 2.6 Docness................................................. -
Návrh a Implementace Rozšíření Do Systému Phabricator
Masarykova univerzita Fakulta informatiky Návrh a implementace rozšíření do systému Phabricator Diplomová práce Lukáš Jagoš Brno, podzim 2019 Masarykova univerzita Fakulta informatiky Návrh a implementace rozšíření do systému Phabricator Diplomová práce Lukáš Jagoš Brno, podzim 2019 Na tomto místě se v tištěné práci nachází oficiální podepsané zadání práce a prohlášení autora školního díla. Prohlášení Prohlašuji, že tato diplomová práce je mým původním autorským dílem, které jsem vypracoval samostatně. Všechny zdroje, prameny a literaturu, které jsem při vypracování používal nebo z nich čerpal, v práci řádně cituji s uvedením úplného odkazu na příslušný zdroj. Lukáš Jagoš Vedoucí práce: Martin Komenda i Poděkování Srdečně chci na tomto místě poděkovat vedoucímu mé diplomové práce RNDr. Martinu Komendovi, Ph.D. za cenné náměty a odborné vedení. Dále chci poděkovat Mgr. Matěji Karolyi za všestrannou po- moc při implementaci praktické části práce a Ing. Mgr. Janu Krejčímu za zpřístupnění testovacího serveru a technickou podporu. iii Shrnutí Diplomová práce se zabývá nástroji pro projektové řízení. V teore- tické části jsou vymezeny pojmy projekt a projektové řízení. Poté jsou představeny vybrané softwarové nástroje pro projektové řízení a je provedeno jejich srovnání. Pozornost je zaměřena na systém Phabrica- tor, který je v práci detailně popsán. V praktické části je navrženo rozšíření Phabricatoru na základě analýzy potřeb a sběru požadavků. Výsledkem je rozšířující modul po- skytující přehledné informace o úkolech z pohledu času a náročnosti, čímž zefektivní jejich plánování a proces týmové spolupráce. iv Klíčová slova projektové řízení, Phabricator, PHP, reportovací modul, SCRUM v Obsah 1 Projektové řízení 3 1.1 Projekt a projektové řízení ..................3 1.2 SW nástroje pro projektové řízení ...............4 1.3 Přehled nástrojů z oblasti řízení projektů ...........6 1.3.1 Phabricator . -
License Agreement
End User License Agreement If you have another valid, signed agreement with Licensor or a Licensor authorized reseller which applies to the specific products or services you are downloading, accessing, or otherwise receiving, that other agreement controls; otherwise, by using, downloading, installing, copying, or accessing Software, Maintenance, or Consulting Services, or by clicking on "I accept" on or adjacent to the screen where these Master Terms may be displayed, you hereby agree to be bound by and accept these Master Terms. These Master Terms also apply to any Maintenance or Consulting Services you later acquire from Licensor relating to the Software. You may place orders under these Master Terms by submitting separate Order Form(s). Capitalized terms used in the Agreement and not otherwise defined herein are defined at https://terms.tibco.com/posts/845635-definitions. 1. Applicability. These Master Terms represent one component of the Agreement for Licensor's products, services, and partner programs and apply to the commercial arrangements between Licensor and Customer (or Partner) listed below. Additional terms referenced below shall apply. a. Products: i. Subscription, Perpetual, or Term license Software ii. Cloud Service (Subject to the Cloud Service Terms found at https://terms.tibco.com/?types%5B%5D=post&feed=recent#cloud-services) iii. Equipment (Subject to the Equipment Terms found at https://terms.tibco.com/?types%5B%5D=post&feed=recent#equipment-terms) b. Services: i. Maintenance (Subject to the Maintenance terms found at https://terms.tibco.com/?types%5B%5D=post&feed=recent#october-maintenance) ii. Consulting Services (Subject to the Consulting terms found at https://terms.tibco.com/?types%5B%5D=post&feed=recent#supplemental-terms) iii. -
Alinex Data Store
Alinex Data Store Read, work and write data structures to differents stores Alexander Schilling Copyright © 2019 - 2021 <a href="https://alinex.de">Alexander Schilling</a> Table of contents Table of contents 1. Home 6 1.1 Alinex Data Store 6 1.1.1 Usage 6 1.1.2 Debugging 6 1.1.3 Module Usage 7 1.1.4 Chapters 7 1.1.5 Support 7 1.2 Command Line Usage 8 1.2.1 Input 8 1.2.2 Output 8 1.2.3 Transform Files 9 1.2.4 Using Definition 9 1.2.5 Examples 9 1.3 Last Changes 10 1.3.1 Version 1.16.0 - (12.05.2021) 10 1.3.2 Version 1.15.0 - (02.01.2021) 10 1.3.3 Version 1.13.0 - (16.06.2020) 10 1.3.4 Version 1.12.0 - (27.01.2020) 10 1.3.5 Version 1.11.0 - (13.01.2020) 11 1.3.6 Version 1.10.0 - (22.11.2019) 11 1.3.7 Version 1.9.1 - (13.11.2019) 11 1.3.8 Version 1.8.0 - (31.10.2019) 11 1.3.9 Version 1.7.0 - (13.10.2019) 11 1.3.10 Version 1.6.0 - (01.10.2019) 11 1.3.11 Version 1.5.0 - (28.08.2019) 12 1.3.12 Version 1.4.0 - (15.08.2019) 12 1.3.13 Version 1.3.0 - (6.08.2019) 12 1.3.14 Version 1.2.0 - (22.06.2019) 13 1.3.15 Version 1.1.0 - (17.05.2019) 13 1.3.16 Version 1.0.0 - (12.05.2019) 13 1.3.17 Version 0.7.0 (29.04.2019) 13 1.3.18 Version 0.6.0 (26.04.2019) 14 1.3.19 Version 0.5.0 (19.04.2019) 14 1.3.20 Version 0.4.0 (17.04.2019) 14 1.3.21 Version 0.3.0 (15.04.2019) 14 - 2/80 - Copyright © 2019 - 2021 <a href="https://alinex.de">Alexander Schilling</a> Table of contents 1.3.22 Version 0.2.0 (12.04.2019) 14 1.3.23 Version 0.1.0 (0t.04.019) 14 1.4 Roadmap 16 1.4.1 Add Protocols 16 1.4.2 Multiple sources 16 1.5 Privacy statement 17 2. -
Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 11 June 2019 doi:10.20944/preprints201906.0091.v1 Peer-reviewed version available at Biomolecules 2019, 9; doi:10.3390/biom9040123 Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood Abheepsa Mishra1, 2,* and Satyahari Dey1 1Plant Biotechnology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India; [email protected] (A.M.); [email protected] (S.D.) 2Department of Internal Medicine, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA *Correspondence: [email protected]; Tel.:+1(518) 881-9196 Abstract Natural products from plants such as, chemopreventive agents attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide based therapeutics have been developed to combat several health disorders including cancers, metabolic disorders, heart-related, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, until date the activities of cyclic peptides towards molecular targets such as protein kinases, proteases, and apoptosis related proteins have never been explored. In this study we explore the in silico kinase and protease inhibitor potentials of cyclosaplin as well as study the interactions of cyclosaplin with other cancer-related proteins. -
D4.1 Source Code and Documentation Repository
D4.1 Source code and documentation repository Co-funded by the Horizon 2020 Framework Programme of the European Union GRANT AGREEMENT NUMBER: 842009 - NIVA DELIVERABLE NUMBER D4.1 DELIVERABLE TITLE Source code and documentation repository RESPONSIBLE AUTHOR Konstantinos Kountouris – Nikolaos Galanis, OPEKEPE Greece 1 GRANT AGREEMENT N. 842009 PROJECT ACRONYM NIVA PROJECT FULL NAME A New IACS Vision in Action STARTING DATE (DUR.) 1/06/2019 ENDING DATE 30/05/2022 PROJECT WEBSITE COORDINATOR Sander Janssen ADDRESS Droevendaalsesteeg 1, Wageningen REPLY TO [email protected] PHONE +31 317 481908 EU PROJECT OFFICER Mrs. Francisca Cuesta Sanchez WORKPACKAGE N. | TITLE WP4 | Knowledge Information System WORKPACKAGE LEADER 8 - AGEA DELIVERABLE N. | TITLE D4.1 | Source code and documentation repository RESPONSIBLE AUTHOR Konstantinos Kountouris – Nikolaos Galanis, OPEKEPE Greece REPLY TO [email protected], [email protected] DOCUMENT URL DATE OF DELIVERY (CONTRACTUAL) 31 August 2019 (M3) DATE OF DELIVERY (SUBMITTED) 30 September 2019 (M4) VERSION | STATUS V1.0| Final NATURE Report DISSEMINATION LEVEL PUBLIC Konstantinos Kountouris – Nikolaos Galanis - Ioannis Andreou, OPEKEPE AUTHORS (PARTNER) Greece 2 VERSION MODIFICATION(S) DATE AUTHOR(S) Konstantinos Kountouris – Nikolaos Galanis - Ioannis 1.0 Final version 24 August 2019 Andreou, OPEKEPE Greece 3 Table of Contents Choosing the proper tool ........................................................................................ 5 Requirements and Assumptions ...........................................................................