From 2011.igem.org

Revision as of 19:43, 24 September 2011

Introduction

In conjunction with our project, we have developed software tools designed to manage an electronic laboratory notebook (ELN) which is specifically tailored to interact with the iGEM Wiki page. The following tools were designed or adapted for use in our ELN software:

1. Labnote: Labnote is the main ELN application. Labnote was written from scratch by Nathan Davis.
2. Rtf2WikiMarkup: This application is a command-line tool designed to convert the RTF entries produced by Labnote into valid Wiki Markup suitable for upload to a MediaWiki-powered site. Rtf2WikiMarkup is an extension of the Rtf Converter framework written by Jani Giannoudis which can be found at [http://www.codeproject.com/KB/recipes/RtfConverter.aspx?msg=3093850 http://www.codeproject.com/KB/recipes/RtfConverter.aspx?msg=3093850].
3. WikiBot: This application is a command-line tool which allows automated uploading of files and pages to a MediaWiki-powered site. This application utilizes a modified version of the DotNetWikiBot framework which can be found at [http://sourceforge.net/projects/dotnetwikibot http://sourceforge.net/projects/dotnetwikibot].

Below you can find the source code for these applications as well as a compiled distribution which should run "out of the box" on Windows platforms. NOTE: all files have been scanned for viruses prior to uploading. Please use a program to verify the checksums listed below before opening any files.

Labnote

Labnote is written in C# and requires that the [http://www.microsoft.com/download/en/details.aspx?id=17851 Microsoft .NET Framework 4.0] be installed on your computer. Labnote has the following dependencies:

1. RicherTextBox: Labnote depends upon the [http://www.codeproject.com/KB/edit/RicherTextBox.aspx RicherTextBox custom user control] originally written by Svetoslav Svov and modified by Nathan Davis.
2. csharp-sqlite: Labnote depends upon the [http://code.google.com/p/csharp-sqlite CSharp-SQLite] framework.

The Labnote source code can be found [http://phyrtech.com/igem/labnote.zip here]. This source code is distributed under the GPL 3.0 license found within the zip file.

Rtf2WikiMarkup

Rtf2WikiMarkup is a command-line utility written specifically for use with Labnote. Rtf2WikiMarkup is capable of receiving an RTF document and converting it into a plain text Wiki Markup file along with any accompanying images that might be a part of the RTF document. Rtf2WikiMarkup was written by Nathan Davis and is an adaptation of the [http://www.codeproject.com/KB/recipes/RtfConverter.aspx?msg=3093850 Rtf Converter framework] written by Jani Giannoudis.

The Rtf2WikiMarkup source code can be found [http://phyrtech.com/igem/Rtf2WikiMarkup_src.zip here]. This source code is distributed under the GPL 3.0 license.

WikiBot

WikiBot is a command-line utility which is capable of uploading image files and page text to a MediaWiki-powered site. WikiBot was written by Nathan Davis and utilizes a modified version of the [http://sourceforge.net/projects/dotnetwikibot/ DotNetWikiBot framework].

WikiBot depends upon a component of the Phyrtech Framework, the source code for which can be found [http://phyrtech.com/igem/Phyrtech_Framework.zip here].

The WikiBot source code can be found [http://phyrtech.com/igem/WikiBot.zip here]. This source code is distributed under the GPL 3.0 license.

Compiled Distribution

For your convenience, a zip file containing the compiled versions of Labnote, Rtf2WikiMarkup, and WikiBot along with their dependencies is provided [http://phyrtech.com/igem/Labnote_dist.zip here].

Checksums

Checksums for: Phyrtech_Framework.zip

MD5: d7f60b9a7380ae5193b33fd1e28996cb

SHA-1: 33bbc30bbf2c5f990b53c872c73390a98271e50f

SHA-256: c5a7af78940ffb2216ab156beca9a15cd2b1f2e2d83a5bb2c32c64bbe5c6bcbe

Checksums for: WikiBot.zip

MD5: 4270139ff0db50f77cac31e94dc8a862

SHA-1: aa9a374e67bd2463908e6806e26d27fa79650998

SHA-256: b38a9c97dc94d2bd1a4c9b232a68060ccd3fd5f60114747066108bffa4cbfcb4

Checksums for: Labnote_dist.zip

MD5: 556c97bd384deaaf3ff950b24e7e6dc7

SHA-1: 62c829f5dda6edc4b9e28a5dec6368427cd7ba0e

SHA-256: 7f9558632b3aaa73e8bffd24e0467465155cc6904e35d470475f9762b63ff5cd

Checksums for: labnote.zip

MD5: 33365f4c3f702eeb38c40d005dca9cfc

SHA-1: 0afe28bd099a962fd4d5cda39d3a355d5e544da5

SHA-256: a44781d8a978ce26fc490f3931510dac45e2256524a402c80ae5c84aa8e5091b

Checksums for: Rtf2WikiMarkup_src.zip

MD5: d60badfbf3a5a202b916365fe8b57d5e

SHA-1: a04bb7c74353858113fecd613e80b1905536cd62

SHA-256: 49dd081bcfd0820b8e98b7abe59b97fc014e622dcc67c4d2cb2d6253545936cd

240px