Visit E Asy to Use

Total Page：16

File Type：pdf, Size：1020Kb

FFrreeee!! EEaassyy ttoo uussee PPoowweerrffuull What is Vigyaan? What is VigyaanCD? Vigyaan Home Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. VigyaanCD is a live Linux CD containing all the Downloads required software to boot the computer with ready to use modeling software. Suitable for beginners and experts. Demos and Tutorials What software is available on VigyaanCD? Biology Tools At present the following ready to use software comes on VigyaanCD: Arka/GP, Artemis, Bioperl, BLAST (NCBI-tools), ClustalW/ClustalX, Cn3D, EMBOSS Genomes tools, Garlic, Glimmer, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, Jmol, MPQC, MUMer, NJPlot, Open Babel, Octave, PSI3, Chemistry Tools PyMOL, Ramachandran plot viewer, Rasmol, Raster3D, Seaview, TINKER, XDrawChem, Xmgr and GNU C/C++/Fortran compilers and additional Linux Other Tools tools (such as ps2pdf) are also available. FAQs How much does it cost? VigyaanCD is free and distributed under GPL. Obtain your free copy from the Vigyaan Wizard project home-page: http://www.vigyaanCD.org/ Sceenshots Do I need to install VigyaanCD on my computer to run it? No. You can directly run VigyaanCD by booting the computer from CD-ROM About Us/ without installing anything on your hard-disk. When done, simply remove the Contact VigyaanCD and reboot computer normally. What do I need to run VigyaanCD? You need to download the latest Vigyaan ISO and burn it on to a CD. VigyaanCD will work on most PCs with Intel-compatible CPU with a bootable CD-ROM drive Do you have Demos and Tutorials? Yes. Simple startup demos and detailed tutorials are available on CD. Do I need to have/install Windows or Linux on my computer to use VigyaanCD? No. All the software needed to start the workbench are present on the CD. Developed by: What if I have more questions? Pratul K. Agarwal Please visit the project home-page for more details or write to us. visit hhttttpp::////wwwwww..vviiggyyaaaannCCDD..oorrgg//.

Copy Link

Recommended publications

User Guide of Computational Facilities
Physical Chemistry Unit Departament de Quimica User Guide of Computational Facilities Beta Version System Manager: Marc Noguera i Julian January 20, 2009 Contents 1 Introduction 1 2 Computer resources 2 3 Some Linux tools 2 4 The Cluster 2 4.1 Frontend servers . 2 4.2 Filesystems . 3 4.3 Computational nodes . 3 4.4 User’s environment . 4 4.5 Disk space quota . 4 4.6 Data Backup . 4 4.7 Generation of SSH keys for automatic SSH login . 4 4.8 Submitting jobs to the cluster . 5 4.8.1 Typical queue system commands . 6 4.8.2 HomeMade scripts . 6 4.8.3 Create your own submit script . 6 4.8.4 Submitting Parallel Calculations . 7 5 Available Software 9 5.1 Chemisty software . 9 5.2 Development Software . 10 5.3 How to use the software . 11 5.4 Non-default environments . 11 6 Your Linux Workstation 11 6.1 Disk space on your workstation . 12 6.2 Workstation Data Backup . 12 6.3 Running virtual Windows XP . 13 6.3.1 The Windows XP Environment . 13 6.4 Submitting calculations to your dekstop . 13 6.5 Network dependent structure . 14 7 Your WindowsXP Workstation 14 7.1 Workstation Data Backup . 14 8 Frequently asked questions 14 1 Introduction This User Guide is aimed to the standard user of the computer facilities in the ”Unitat de Quimica Fisica” in the Universitat Autnoma de Barcelona. It is not assumed that you have a knowledge of UNIX/Linux. However, you are 1 encouraged to take a close look to the linux guides that will be pointed out.
[Show full text]
Chem3d Download Mac
1 / 2 Chem3d Download Mac ChemSketch for Mac OS X, download best alternative solutions carefully chosen by our editors and user community.. Supported in Macintosh for Netscape (4.0+ only). No Mac support for Internet Explorer, Safari, or OSX browsers. To Download and Install Chem3D Plug-in: Go to .... On a Macintosh browser, you can switch between Chime and Chem3D plugins using the Edit/Preferences/Applications menu. On Windows, switching between .... Mac users interested in Chemdraw ultra free generally download: CS ChemDraw Ultra 12.0. ChemDraw is the industry leader of chemical drawing programs.. Aug 25, 2020 — To download ChemDraw, you'll need to create a personal account ... ChemDraw - Activation Help - Win - Mac I get an error message containing, “ … ... Day 2: Part III: ChemDraw; Part IV: Chem3D; Remember that you can .... This includes Chem3D, for Windows only. The licence allows you to download the software to your own PC (not available for Mac). The version currently .... ChemDraw 8 Ultra, Windows And Macintosh Versions. Chemdraw ultra Most people looking for Chemdraw ultra downloaded: ChemDraw Ultra. Download. on .... Chem3D does not show a pair of electrons that is part of an aromatic system. ... well as for the Mac platform and can be downloaded by students and coworker of ... The license is for both the Windows and Mac versions of the software. ... are available in the Windows version (such as Chem3D Pro and E-Notebook Pro). ... Download the software installer for your operating system (Windows or Mac) and .... May 26, 2020 — Accessing and Installing ChemDraw (Mac) or ChemOffice (Windows) ... ChemDraw Professional; ChemDraw for Excel; Chem3D; ChemFinder ..
[Show full text]
Optimizing the Use of Open-Source Software Applications in Drug
DDT • Volume 11, Number 3/4 • February 2006 REVIEWS TICS INFORMA Optimizing the use of open-source • software applications in drug discovery Reviews Werner J. Geldenhuys1, Kevin E. Gaasch2, Mark Watson2, David D. Allen1 and Cornelis J.Van der Schyf1,3 1Department of Pharmaceutical Sciences, School of Pharmacy,Texas Tech University Health Sciences Center, Amarillo,TX, USA 2West Texas A&M University, Canyon,TX, USA 3Pharmaceutical Chemistry, School of Pharmacy, North-West University, Potchefstroom, South Africa Drug discovery is a time consuming and costly process. Recently, a trend towards the use of in silico computational chemistry and molecular modeling for computer-aided drug design has gained significant momentum. This review investigates the application of free and/or open-source software in the drug discovery process. Among the reviewed software programs are applications programmed in JAVA, Perl and Python, as well as resources including software libraries. These programs might be useful for cheminformatics approaches to drug discovery, including QSAR studies, energy minimization and docking studies in drug design endeavors. Furthermore, this review explores options for integrating available computer modeling open-source software applications in drug discovery programs. To bring a new drug to the market is very costly, with the current of combinatorial approaches and HTS. The addition of computer- price tag approximating US$800 million, according to data reported aided drug design technologies to the R&D approaches of a com- in a recent study [1]. Therefore, it is not surprising that pharma- pany, could lead to a reduction in the cost of drug design and ceutical companies are seeking ways to optimize costs associated development by up to 50% [6,7].
[Show full text]
Pipenightdreams Osgcal-Doc Mumudvb Mpg123-Alsa Tbb
pipenightdreams osgcal-doc mumudvb mpg123-alsa tbb-examples libgammu4-dbg gcc-4.1-doc snort-rules-default davical cutmp3 libevolution5.0-cil aspell-am python-gobject-doc openoffice.org-l10n-mn libc6-xen xserver-xorg trophy-data t38modem pioneers-console libnb-platform10-java libgtkglext1-ruby libboost-wave1.39-dev drgenius bfbtester libchromexvmcpro1 isdnutils-xtools ubuntuone-client openoffice.org2-math openoffice.org-l10n-lt lsb-cxx-ia32 kdeartwork-emoticons-kde4 wmpuzzle trafshow python-plplot lx-gdb link-monitor-applet libscm-dev liblog-agent-logger-perl libccrtp-doc libclass-throwable-perl kde-i18n-csb jack-jconv hamradio-menus coinor-libvol-doc msx-emulator bitbake nabi language-pack-gnome-zh libpaperg popularity-contest xracer-tools xfont-nexus opendrim-lmp-baseserver libvorbisfile-ruby liblinebreak-doc libgfcui-2.0-0c2a-dbg libblacs-mpi-dev dict-freedict-spa-eng blender-ogrexml aspell-da x11-apps openoffice.org-l10n-lv openoffice.org-l10n-nl pnmtopng libodbcinstq1 libhsqldb-java-doc libmono-addins-gui0.2-cil sg3-utils linux-backports-modules-alsa-2.6.31-19-generic yorick-yeti-gsl python-pymssql plasma-widget-cpuload mcpp gpsim-lcd cl-csv libhtml-clean-perl asterisk-dbg apt-dater-dbg libgnome-mag1-dev language-pack-gnome-yo python-crypto svn-autoreleasedeb sugar-terminal-activity mii-diag maria-doc libplexus-component-api-java-doc libhugs-hgl-bundled libchipcard-libgwenhywfar47-plugins libghc6-random-dev freefem3d ezmlm cakephp-scripts aspell-ar ara-byte not+sparc openoffice.org-l10n-nn linux-backports-modules-karmic-generic-pae
[Show full text]
Bringing Open Source to Drug Discovery
Bringing Open Source to Drug Discovery Chris Swain Cambridge MedChem Consulting Standing on the shoulders of giants • There are a huge number of people involved in writing open source software • It is impossible to acknowledge them all individually • The slide deck will be available for download and includes 25 slides of details and download links – Copy on my website www.cambridgemedchemconsulting.com Why us Open Source software? • Allows access to source code – You can customise the code to suit your needs – If developer ceases trading the code can continue to be developed – Outside scrutiny improves stability and security What Resources are available • Toolkits • Databases • Web Services • Workflows • Applications • Scripts Toolkits • OpenBabel (htttp://openbabel.org) is a chemical toolbox – Ready-to-use programs, and complete programmer's toolkit – Read, write and convert over 110 chemical file formats – Filter and search molecular files using SMARTS and other methods, KNIME add-on – Supports molecular modeling, cheminformatics, bioinformatics – Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry – Written in C++ but accessible from Python, Ruby, Perl, Shell scripts… Toolkits • OpenBabel • R • CDK • OpenCL • RDkit • SciPy • Indigo • NumPy • ChemmineR • Pandas • Helium • Flot • FROWNS • GNU Octave • Perlmol • OpenMPI Toolkits • RDKit (http://www.rdkit.org) – A collection of cheminformatics and machine-learning software written in C++ and Python. – Knime nodes – The core algorithms and data structures are written in C ++. Wrappers are provided to use the toolkit from either Python or Java. – Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
[Show full text]
Free Chemdraw Program
Free chemdraw program click here to download ACD/Labs extension for ChemDraw, checkmark. Technical Support Free access to site licenses of ACD/ChemSketch Freeware are available. Popular Alternatives to ChemDraw for Windows, Linux, Mac, iPhone, iPad and XDrawChem is a free software program for drawing chemical. The PerkinElmer Available Chemicals Exchange, ChemACX, is a comprehensive online chemical database catalog for chemical products containing. ChemDraw Prime is the complete entry-level structure drawing program, with all the tools you need to quickly create chemically intelligent, publication-ready. ChemDraw features stereochemistry, atom numbering, structure & style templates, a large choice of bonds & arrows, full color drawing, and more. You can download ChemDraw Ultra from our software library for free. Our built-in antivirus checked this download and rated it as virus free. ChemDraw Pro is available as a free download on our software library. The software lies within Education Tools, more precisely Science. ChemDraw Pro is industry leading molecules drawing software. Download ChemDraw Free Pro full version with product key. Chemsketch is an all-purpose chemical drawing and graphics software. Use templates or free-hand. Click and draw molecules, ions, stereobonds, text, polygons. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles. Free ChemBioDraw Ultra Software. ChemBioDraw Ultra The license is for both the Windows and Mac versions of the software. Please note that the Mac. ChemDraw and Symyx Draw file formats (skc, cdx) are also recognized by Marvin. Structures from image files can be converted in MarvinSketch using the free.
[Show full text]
Drawing Software in Chemistry: Free/Open Source (Foss), Freeware- a Short Review
International Journal of Innovative Research in Science, Engineering and Technology (IJIRSET) || e-ISSN: 2319-8753, p-ISSN: 2320-6710| www.ijirset.com | Impact Factor: 7.512| || Volume 9, Special Issue 2, October 2020 || 3rd International Conference on Emerging Trends in Science, Technology and Mathematics [ICETSTM 2020] 18th September 2020 Organized by Department of Computer Science, Parvathy's Arts and Science College, Dindigul, Tamilnadu, India Drawing Software in Chemistry: Free/Open Source (Foss), Freeware- A Short Review Arun Luiz T Department of Chemistry, Sri Sivasubramaniya Nadar College of Engineering, Old Mahabalipuram Road, Kalavakkam, Tamilnadu, India ABSTRACT: COVID-19 pandemic made online education in vogue. It has become mandatory for chemistry community to know about various tools, which are available for their disposal. This short review lists various software, which can be used for drawing structures, writing equations etc. These software include Free/Open Source (FOSS) and freeware that can be easily downloaded from internet free of cost for academic purposes. KEYWORDS: Software, Drawing, FOSS, Freeware I. INTRODUCTION The World Health Organization (WHO) declared the COVID-19 outbreak as a pandemic on 11 March 2020 [1]. Most of the governments all around the world temporarily closed down all educational institutions to prevent to the spreading of virus. According to Wikipedia, by the end of July 2020, around 1.7 billion learners were affected by this lockdown [2]. Most of the schools, colleges and universities were forced to switch over to “online mode” of synchronous and asynchronous teaching and learning. UNESCO recommended the use of distance learning programs and open educational applications and platforms for students and teacher for better teaching learning experience [2].
[Show full text]
Modularitet Och Objektorientering
Uppsala universitet Institutionen för informatik och media Modularitet och objektorientering Byggandet av ett program som kan visa en molekyl Lars Tedenborg Examensarbete C Höstterminen 2010 2011-01-04 Abstract The development of IT systems is usually accomplished by some form of system development methodology. It can be performed as the waterfall method, where each phase is completed before the next begins. One of the reasons to follow a development methodology is that the process is more structured, faster and that the product will have higher quality. One risk of not using a system development approach is that the code can be unstructured and difficult to maintain. This paper describes an alternative method in which the development occurred without the use of any system development methodology. This has been possible because there was a clear goal of the program that should be developed. The goal was to read a molfile and from the information stored in the file plot the molecular structure. The appearance of the molecule has been fine-tuned as more features are added. A molfile is able to store all the information about the different characteristics a molecule can have. Not all molecules containing all the properties. Development has proceeded as follows: Each property has been classified as an object and then implemented. The whole way from reading the property in the file into the computer program and then interpret the information to plot the property as a part of the molecule. The most important programming principle has been to develop the program as a number of more or less independent modules for the system to have high modularity.
[Show full text]
User Guide of Computational Facilities
Physical Chemistry Unit, Departament de Química User Guide of Computational Facilities An User Guide for the standard user of the computer facilities in the ”Unitat de Química Física” in the Universitat Autònoma de Barcelona Marc Noguera i Julián and Carles Acosta i Silva 23/02/2011 Table Of Contents 1 Introduction ................................................................................................................................ 4 2 Computer resources ................................................................................................................... 4 3 Some Linux tools ........................................................................................................................ 5 4 The Cluster ................................................................................................................................. 6 4.1 Frontend servers ................................................................................................................. 6 4.2 Filesystems .......................................................................................................................... 6 4.3 Computational nodes .......................................................................................................... 7 4.4 User’s environment ............................................................................................................. 9 4.5 Disk space quota ................................................................................................................. 9 4.6
[Show full text]
Bringing Open Source to Drug Discovery
Bringing Open Source to Drug Discovery Chris Swain Cambridge MedChem Consulting Standing on the shoulders of giants • There are a huge number of people involved in writing open source software • It is impossible to acknowledge them all individually • The slide deck will be available for download and includes 25 slides of details and download links – Copy on my website www.cambridgemedchemconsulting.com Why us Open Source software? • Allows access to source code – You can customise the code to suit your needs – If developer ceases trading the code can continue to be developed – Outside scrutiny improves stability and security What Resources are available • Toolkits • Databases • Web Services • Workflows • Applications • Scripts Toolkits • OpenBabel • R • CDK • OpenCL • RDkit • SciPy • Indigo • NumPy • ChemmineR • Pandas • Helium • Flot • FROWNS • GNU Octave • Perlmol • OpenMPI Toolkits • OpenBabel (htttp://openbabel.org) is a chemical toolbox – Ready-to-use programs, and complete programmer's toolkit – Read, write and convert over 110 chemical file formats – Filter and search molecular files using SMARTS and other methods, KNIME add-on – Supports molecular modeling, cheminformatics, bioinformatics – Organic chemistry, inorganic chemistry, solid-state materials, nuclear chemistry – Written in C++ but accessible from Python, Ruby, Perl, Shell scripts… Toolkits • RDKit (http://www.rdkit.org) – A collection of cheminformatics and machine-learning software written in C++ and Python. – Knime nodes – The core algorithms and data structures are written in C ++. Wrappers are provided to use the toolkit from either Python or Java. – Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
[Show full text]
Instructions Manuals Xdrawchem.Pdf
Instructions Manuals Xdrawchem Wikipedia:Manual of Style/Chemistry/Structure drawing program called WinDrawChem (the Windows version of XDrawChem) that appears to work well. Link. xdrawchem · packages.ubuntu.com/xdrawchem Ubuntu Maverick for Research - Installation, pointers to many relevant programs on Ubuntu 10.10. To install xdrawchem just follow these instructions. × Are you having problems? You can always remove xdrawchem again by following the instructions at this. XDrawChem is a drawing application designed for drawing and analyzing methods & parameters, easily generate reports & certificates, fine tune user rights. package in Ubuntu Trusty. Installation instructions. Installing xdrawchem package in Ubuntu Trusty is as easy as running: apt-get install xdrawchem. 1 Science Writing Manuals and Style Guides, 2 Science Writing Tutorials and The Chemistry Style Manual 2nd revised ed., 2004 by Kieran F. Lim (Deakin. Instructions Manuals Xdrawchem Read/Download Documentation · FAQ · Handbook · Porter's Handbook · Developer's Handbook · Manual Pages · Documentation Project Primer · All Books and Articles. XDrawChem _xdrawchem.sourceforge.net/_ Open (GukLogFile) · GAMESS-UK Punchfile. GAMESS - the US version GAMESS manual · (Log_file). XDrawChem free download, 100% safe and virus free download from Softonic. More info about this program · Read user reviews (2) · See screenshot. User Interface. Web-based, Win32 (MS Windows), X Window System (X11) intuitive molecular editor and visualization tool. Icon · SketchEl · Icon. XDrawChem. 2 In Progress. 2.1 LabPlot, 2.2 XDrawChem Notes aMule is there but it looks very bad in KDE and in general its user interface is quite bad. We can do much. It can read and write MDL Molfiles to allow sharing between XDrawChem and A high power gift from Vancouver (Canada) with an extensive user's guide.
[Show full text]
The Table of Equivalents / Replacements / Analogs of Windows Software in Linux
The table of equivalents / replacements / analogs of Windows software in Linux. Last update: 16.07.2003, 31.01.2005, 27.05.2005, 04.12.2006 You can always find the last version of this table on the official site: http://www.linuxrsp.ru/win-lin-soft/. This page on other languages: Russian, Italian, Spanish, French, German, Hungarian, Chinese. One of the biggest difficulties in migrating from Windows to Linux is the lack of knowledge about comparable software. Newbies usually search for Linux analogs of Windows software, and advanced Linux-users cannot answer their questions since they often don't know too much about Windows :). This list of Linux equivalents / replacements / analogs of Windows software is based on our own experience and on the information obtained from the visitors of this page (thanks!). This table is not static since new application names can be added to both left and the right sides. Also, the right column for a particular class of applications may not be filled immediately. In future, we plan to migrate this table to the PHP/MySQL engine, so visitors could add the program themselves, vote for analogs, add comments, etc. If you want to add a program to the table, send mail to winlintable[a]linuxrsp.ru with the name of the program, the OS, the description (the purpose of the program, etc), and a link to the official site of the program (if you know it). All comments, remarks, corrections, offers and bugreports are welcome - send them to winlintable[a]linuxrsp.ru. Notes: 1) By default all Linux programs in this table are free as in freedom.
[Show full text]