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  • Computer Center - National Center for Macromolecular Imaging - Baylor College of Medicine - Houston, TX
    DOWNLOADS Software Movies PUBLICATIONS Journal Covers NCMI Publications Magazine Features EVENTS Workshops and Symposiums Archived Video Lectures LINKS NCMI Associated Centers Electron Microscopy Sites Supporting Agencies Computational and Structural Biology Online Journals COLLABORATIONS NCMI Computer Center Projects hosted on this server EMAN EMAN2 EMEN2 SPARX BCM Home BCM Intranet Privacy Notices Contact BCM BCM Site Map 1998 2007 Baylor College of Medicine National Center for Macromolecular Imaging NCMI Intranet Room

    Original URL path: http://blake.bcm.edu/ (2013-03-17)
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  • EMEN2 - EMAN Wiki
    based on plain text descriptions of experimental protocols These protocols may be local and describe techniques and data within a single lab group An EMEN2 installation can itself act as a resource providing public access to selected protocols and data While originally developed to serve the needs of the cryo EM community we believe EMEN2 s architecture provides an excellent foundation for many other scientific endeavors EMEN2 is developed using all open source technologies The core database is written in the Python programming language with BerkeleyDB providing a robust embedded database back end The infrastructure is highly modular permitting new ontologies to be fully implemented using only it s Web 2 0 interface In addition there is a remote API available for client applications The included EMDash program is a standalone GUI tool for equipment integration currently used to upload data transparently from our electron microscopes as it is being collected as well as integrate with other lab equipment The EMEN2 server itself can be extended in a similar way by writing custom Python modules which can expose additional views to the Web interface or new methods to the API A full ontology for cryo EM has been established for internal use and has been in active use at the NCMI for 3 years It is used to archive all data at the center and currently provides services for over 750 users with over 16 terabytes of data in 460 000 records As an example of its extensibility and ontology mapping capabilities we have developed a module for harvesting the database and producing PDB compliant XML files which can be used to seed a structure deposition to EMDatabank org EMEN2 Demo There is a publicly accessible read only EMEN2 installation for accessing the NCMI s public datasets http ncmi bcm

    Original URL path: http://blake.bcm.edu/emanwiki/EMEN2 (2013-03-17)
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  • EMAN - EMAN Wiki
    docs are editable by any user that has registered an account on the server The new Wiki documentation is here EMAN1 EMAN2 Which link to follow In most cases the EMAN2 link While still fully functional EMAN1 is no longer actively developed EMAN2 is capable of replacing virtually every aspect of processing that might have been done previously in EMAN1 and in most cases with more accuracy and less effort What is EMAN EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community though it is beginning to be used in other fields as well EMAN has a particular focus on performing a task known as single particle reconstruction In this method images of nanoscale molecules and molecular assemblies embedded in vitreous glassy ice are collected on a transmission electron microscope then processed using EMAN to produce a complete 3 D recosntruction at resolutions now approaching atomic resolution For low resolution structures 2 nm this may require 8 hours of computer processing and a few thousand particles For structures aimed at 0 5 nm or better resolution hundreds of thousands of particles and hundreds of thousands of CPU hours on large computational clusters may be required Indeed EMAN is often used in supercomputing facilities as a test application for large scale computing Scientific image processing is distinguished from typical Photoshop image processing in that it is analytical in nature Images processed in EMAN are floating point greyscale images That is the pixel values in the images are represented as real numbers not as small integers typical GIF JPG PNG images are limited to integral values from 0 255 for each pixel Processing often includes complex image processing operations in Fourier or Wavelet space EMAN was first released in 1999 and has been under

    Original URL path: http://blake.bcm.edu/emanwiki/EMAN (2013-03-17)
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  • Login - EMAN Wiki
    Cache Check Spelling Like Pages Local Site Map Rename Page Delete Page Subscribe User Remove Spam Revert to this revision Package Pages Sync Pages Load Save SlideShow Name Password If you do not have an account you can create one now Forgot your password Immutable Page Comments Info Attachments More Actions Raw Text Print View Render as Docbook Delete Cache Check Spelling Like Pages Local Site Map Rename Page Delete

    Original URL path: http://blake.bcm.edu/emanwiki/EMEN2?action=login (2013-03-17)
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  • Title Search: "linkto:"EMEN2"" - EMAN Wiki
    here to perform a full text search with your search terms Results 1 13 of 13 results out of about 17057 pages 5 17 seconds EMAN2 4 6k rev 74 current last modified 2013 02 25 13 57 24 EMEN2 3 5k rev 61 current last modified 2012 10 17 00 01 13 EMEN2 BackupsOld 2 0k rev 30 current last modified 2010 09 22 07 18 44 EMEN2 Dependencies 2 1k rev 44 current last modified 2012 07 11 02 20 36 EMEN2 EMAN2 Integration 2 5k rev 9 current last modified 2010 04 21 05 47 46 EMEN2 Install 2 9k rev 55 current last modified 2012 07 11 11 52 50 EMEN2 Install Example 3 1k rev 9 current last modified 2012 07 11 11 52 40 EMEN2 Public Data Server 2 6k rev 8 current last modified 2010 03 29 09 14 05 EMEN2 Startup 2 4k rev 13 current last modified 2012 07 31 21 47 44 EMEN2 User Guide 1 0k rev 11 current last modified 2010 04 21 05 04 45 EMEN2 emen2 client py 6 3k rev 27 current last modified 2011 05 20 15 58 47 EMEN2 Wiki 0 1k rev

    Original URL path: http://blake.bcm.edu/emanwiki/EMEN2?action=fullsearch&context=180&value=linkto%3A%22EMEN2%22 (2013-03-17)
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  • RecentChanges - EMAN Wiki
    03 Upload of attachment lecture 13 pdf 04 Upload of attachment chat py 2013 02 15 SPT Spt 22 00 jgalaz 2013 02 06 EMAN2 Video Tutorials 16 28 SteveLudtke 2013 01 30 EMAN2 Symmetry 21 09 SteveLudtke EMAN2 Programs e2refinetorelion3d e2refinetorelion3dtutorial 20 13 StephenMurray 2013 01 25 EMAN2 Programs e2projectmanager 19 10 StephenMurray marks older pages that have at least one backup version stored click for an author diff

    Original URL path: http://blake.bcm.edu/emanwiki/RecentChanges (2013-03-17)
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  • HelpContents - EMAN Wiki
    HelpForUsers is help for users who are new to a MoinMoin wiki HelpOnAdministration how to configure and maintain a MoinMoin wiki HelpIndex is a list of all available help pages Fulltext search is available on FindPage If you find any errors on the help pages please describe them on HelpErrata Please do not edit or create help pages in other wikis than Moin Master see HelpContents because the pages from

    Original URL path: http://blake.bcm.edu/emanwiki/HelpContents (2013-03-17)
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  • EMAN1 - EMAN Wiki
    will likely never be as complete as the EMAN2 Wiki EMAN1 is gradually being deprecated in favor of EMAN2 and the EMAN1 static documentation is fairly complete Please feel free to contribute your own comments and ideas Download EMAN Current stable version Nightly builds Installation Instructions Tips Documentation Static non Wiki Documentation Overview of single particle reconstruction Documentation of individual programs Python C Library Docs EMAN2 preferred Ask your questions here Frequently Asked Questions add your general questions here Questions on specific projects add your project specific questions here About EMAN EMAN is a suite of scientific image processing tools aimed primarily at the transmission electron microscopy community though it is beginning to be used in other fields as well For example it can do an admirable job aligning images for amateur astronomers EMAN has a particular focus on performing a task known as single particle reconstruction In this method images of nanoscale molecules and molecular assemblies embedded in vitreous glassy ice are collected on a transmission electron microscope then processed using EMAN to produce a complete 3 D recosntruction at resolutions now approaching atomic resolution For low resolution structures 2 nm this may require 8 hours of computer processing

    Original URL path: http://blake.bcm.edu/emanwiki/EMAN1 (2013-03-17)
    Open archived version from archive