Differences between revisions 69 and 78 (spanning 9 versions)
Revision 69 as of 2013-04-18 06:35:18
Size: 3433
Editor: IanRees
Comment:
Revision 78 as of 2013-04-18 07:04:25
Size: 3572
Editor: IanRees
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
{{attachment:emen2logo.png|EMEN2|width=250}} {{attachment:emen2logo.png|EMEN2|width="250"}}
Line 4: Line 4:
Line 7: Line 6:
Please note, this is NOT the related [[EMAN2]] image processing system.

Structural and computational biologists frequently work with complex data sets assembled from diverse experimental sources, public resources, and analysis methods. Archiving and mining these data sets with their complicated interrelationships remains a persistent challenge, particularly with “open science” initiatives to make entire workflows, including all raw and intermediate data, available with publications. 
Structural and computational biologists frequently work with complex data sets assembled from diverse experimental sources, public resources, and analysis methods. Archiving and mining these data sets with their complicated interrelationships remains a persistent challenge, particularly with “open science” initiatives to make entire workflows, including all raw and intermediate data, available with publications.
Line 15: Line 12:
You can read about EMEN2 in the manuscript [[http://www.ncbi.nlm.nih.gov/pubmed/23360752|EMEN2: an object oriented database and electronic lab notebook]]. You can read about EMEN2 in the manuscript:

[[http://www.ncbi.nlm.nih.gov/pubmed/23360752|Rees, I., Langley, E., Chiu, W., & Ludtke, S.J. (2013). EMEN2: an object oriented database and electronic lab notebook. Microsc Microanal 19, 1-10]]

Please note, this is '''not''' the related [[EMAN2]] image processing system.

== EMEN2 Mailing List ==
 * [[http://groups.google.com/group/emen2|EMEN2 mailing list]]

Please feel free to join the mailing list and ask questions, submit bug reports, or share results.
Line 18: Line 24:
Line 25: Line 30:
== EMEN2 Mailing List ==

 * [[http://groups.google.com/group/emen2|EMEN2 mailing list]]

Please feel free to join the mailing list and ask questions, submit bug reports, or share results.
Line 32: Line 31:
Line 41: Line 39:
 * [[Planning hardware requirements]]  * [[EMEN2/Hardware|Planning hardware requirements]]
Line 44: Line 42:
Line 47: Line 44:
 * [[EMEN2/Backups|Backups and recovery]]
Line 48: Line 47:

* [[EMEN2/api|Public API documentation]] 
 * [[EMEN2/api|Public API documentation]]
Line 56: Line 54:

EMEN2

EMEN2

An extesible, object-oriented electronic lab notebook

Structural and computational biologists frequently work with complex data sets assembled from diverse experimental sources, public resources, and analysis methods. Archiving and mining these data sets with their complicated interrelationships remains a persistent challenge, particularly with “open science” initiatives to make entire workflows, including all raw and intermediate data, available with publications.

To address these needs, we have developed EMEN2, an object-oriented scientific database and electronic notebook. EMEN2 uses a flexible schema 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.

You can read about EMEN2 in the manuscript:

Rees, I., Langley, E., Chiu, W., & Ludtke, S.J. (2013). EMEN2: an object oriented database and electronic lab notebook. Microsc Microanal 19, 1-10

Please note, this is not the related EMAN2 image processing system.

EMEN2 Mailing List

Please feel free to join the mailing list and ask questions, submit bug reports, or share results.

EMEN2 Demo

There is a publicly accessible, read-only EMEN2 installation for accessing the NCMI's public datasets:

http://ncmi.bcm.edu/publicdata/

An overview document has been created to introduce new users to the EMEN2 web interface. It includes a number of screenshots.

EMEN2 Installation and Configuration

EMEN2 Guides

EMEN2 API

EMDash: EMEN2 Client documentation

EMEN2 (last edited 2013-04-22 20:02:57 by IanRees)