Hi Philipp,
Thank you for your interest in BASE.
Some of the information you listed is outdated. Here are updates
you can use.
1) Brief description of BASE:
BASE is a comprehensive free web-based database LIMS solution for
tracking of information and data generated in sequencing and
microarray experiments from sample to analysis. BASE is released under
the GNU General Public License version 3.
2) The reference list could be updated to include
- Häkkinen et al. 2016, https://doi.org/10.1101/038976
- Vallon-Christersson et al. 2009, PMID: 19822003
If only one reference can be retained then you should use
Vallon-Christersson et al.
3) Under miscellaneous you might add that source code is available at
http://base.thep.lu.se? It is open, browsable, searchable, has issue
tracking, and more. Actually predates GitHub ;-)
4) Regarding compliance to standards. We are not actively pursuing
(MIAME) standards compliance, and the public repository upload
functionality is semi-automatic at best.
Cheers,
Jari
On 2019-06-16 14:54, Pugliese, Philipp wrote:
Dear support team,
briefly to me: my name is Philipp Pugliese and I researched for the
Friedrich-Alexander-Universität Erlangen-Nürnberg about functions that
BASE seems to fulfill.
For a congress publication I created a matrix in which BASE is
mentioned. Could you please give me some feedback as to whether the
information I found in the literature is correct or up to date?
The information is:
Brief description of BASE: Is an information and analysis tool for
microarrays that tracks all materials from biosource to raw data to
analyses. The elements can be annotated and used as factors in the
downstream analysis
General
Abbreviation: BioArray Software Environment
FAIR reference: unknown
Note: -
Community
Institution: Lund University
Reference: Saal et al. 2002
PMID: 12186655
Software availability: open source
License: GNU
User mailing list or support: Yes
URL: http://base.thep.lu.se
System requirements
Operating system: Platform independent
DB managing System: MySQL,PostgreSQL
Main programming language: Java
Client-side interface: web browser
Support
Installation procedures: Yes
Configuration documentation: Yes
User documentation: Yes
Regular maintenance: Yes
Miscellaneous
GitHub availability: -
Demo server availability: Yes
Requirements for data management in system biology
Compliance to standards: MIAME
Metadata model: MIAME-related
Automation of data collection: batch import
Upload to public repositories: ArrayExpress, GEO, CIBEX
Extensibility: Java plugins / extentions
Integration with other DMS: via java servlets
Please give me feedback by 30th June 2019 so that your feedback can be
considered until publication.
Thanks in advance and best regards,
Philipp Pugliese
mailto:phil.pugli...@fau.de
P.S.: hope you are the right contact person. If not, could you provide
me the right contact person?
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