A Case Study of Open Source Software Development in Proteomic Area: The LIMS ePims

Abstract

The objective of this paper is to provide an illustrative feedback on development of Open Source software among several partners. We describe the first stage of the design of a specific software package, namely a customized Laboratory Information Management System (LIMS) for biology applications. This software package is structured in several modules which are reusable and can be customized for other applications. In this paper, we address the problem of multi-licensing for the same software tools due to the participation of several partners, the reuse of code source, and the subsequent distribution of this produced software.

Data Acqusition, storage and online retrieval of Chromatography from Automated HPLC for pharmaceutical research applications

“…It has been developed to integrate laboratory equipment with software controls as to achieve an automated and seamless workflow process [7]. Most of commercially available LIMS suffer from limitations [5,6,14]. The specifications of the system are designed based on the manufacturer requirement and depending on their system, the measurement acquired are typically saved in proprietary file formats.…”

“…Most common problem known by LIMS is that users are unable to use the saved format to do offline processing or customized analysis and also users unable to share the saved file in a common format with other users. Works have been done [5][6][7][10][11][12][13][14][15][16][17][18] to overcome the TNF syndrome by producing more common file formats and most of the works prefer XML to be the solution [6,7,10,14,[16][17][18]27] however, some solutions often do not guarantee compatibility with other solutions [34,40,41,44]. The approach of using XML may vary in terms of storing and retrieving data, types of data stored, interfacing the instrument, networking, virtual instrument technique and software used [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][24][25][26][27].…”

“…This work is based on modern automated application process which is an efficient application of data acquisition [11]. Many others custom made LIMS have been developed for this purpose [5][6][7][8][10][11][12][13][14][15][16][17][18].…”

“…In order to justify the measured data taken from AMCOS and the data stored using CONSYS, a comparison have been made with the proprietary software for the reliability and trustworthy of the system. In this paper, literature review had been made in order to compare the existing LIMS [5][6][7][10][11][12][13][14][15][16][17][18], and the experiment that had been done to test the AMCOS and CONSYS. Fig.…”

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

“…To our knowledge, no other open source tool provides support for both web-based specimen requisitions and integration of specimen data with complex experimental results. For example, PASSIM[ 8 ] (and derivatives SLIMS[ 34 ] and SIMBioMS[ 9 ]), caTissue[ 35 ], ePIMS[ 36 ] and BASE[ 10 ]) all provide sample provenance tracking, but none of these allow for web-based sample requests. eOncoLIMS[ 37 ] supports equipment requests and GNomEx[ 38 ] supports experimental work requests, but neither one supports specimen transfers.…”