Re: [basedb-devel] Feedback to BASE information

[Jari H. <jar...@me...>]

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Some of the information you listed is outdated.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:phi...@fa...
> 
> P.S.: hope you are the right contact person. If not, could you provide 
> me the right contact person?
> 
> 
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