SNP Data Management projects
From ICISWiki
Requirements
Steps used for evalution
- Is released on LGPL or equivalent? No then fail, if Yes go to 2.
- Does database schema work on MySQL at least? No then fail, if Yes go to 3.
- Is Java used to connect to the database? No then go 5, if Yes go to 4.
- Test Java code
- Test database schema on MySQL
Conclusions (so far)
At the moment it has not yet been possible to find a system or schema that fits the above criteria for use with ICIS
Current summary of review
| Not suitable |
| Software | Suitability for ICIS integration | Link to software | Reference |
1. License |
2. DBMS |
3. Programming Language | Tested by developer on which OS |
| Golden Helix SNP & Variation Suite | No, Proprietary | link | n/a | Proprietary | N/A | N/A | Windows NT, 2000, XP, XP64, Vista, or Vista64 |
| SNP Processor | Posssible, but SRC and schema links broken | link | ref | Open Source | MySQL or Microsoft Access. | Java | Windows, Linux, Solaris and Mac OS. |
| BC SNP Suites | No, Proprietary | link | n/a | Proprietary | N/A | N/A | Windows®, Mac® and Unix® |
| OpenADAM | Posssible, test database schema only | link | ref | Open Source | PostgreSQL 8.1 | Perl, PHP | Platform independent |
| SNPLims | Posssible, but not can find src code | link | ref | Open Source? | | Python 2.4, Zope 2.9 and Plone 2.5 | tested for Debian |
| TIMS | No schema given | | ref | Open Source | | Visual Basic | The software has been thoroughly tested in Excel 97 and 2000 under various versions of Windows (English versions), Excel 98 of MacOS 9 and Excel X of MacOS X (English versions). |
| SNPHunter | SRC and schema not accessible | link | ref | | | .NET Framwork | Microsoft Windows |
| dbQSNP | Not freely available | link | ref | Available by request | | | Microsoft Windows |
| SNPator | No, Restricted | link | | Restricted to the institute | | | |
| gnpSNP | No possible to donwnload schema to test | link | Genome. 2006 Sep;49(9):1131-9 | Open Source Unlikely | | Looks like PHP? | |
| SNPLIMS (2003) | Possible, but links are broken | link | ref | Open Source | | | Linux |
| SNPFile | Possible schema only, but schema not available as separate download | ref | SNPFile — A software library and file format for large scale association mapping and population genetics studies. J. Nielsen and T. Mailund (2008). BMC Bioinformatics 9(526). | GNU GPL | | C++ | Linux |
| Chado | Only support for SNP markers not actually genotypes | link | | Open Source | | | Unix/Linux/OSX |
| Germinate | No, not enough documentation to test | link | | Open Source (?) | | | |
