Re: [basedb-devel] Feedback to BASE information

[Pugliese, P. <phi...@fa...>]

Hi Jari,

thank you for your quick response, that helps me :)
I'll implement your notes.

Best,
Philipp


--------------------
Am 2019-06-25 11:57, schrieb Jari Häkkinen:
> 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 Some of the information you listed is outdated.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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