Literature DB >> 15930618

HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories.

Jaime Prilusky1, Eric Oueillet, Nathalie Ulryck, Anne Pajon, Julie Bernauer, Isabelle Krimm, Sophie Quevillon-Cheruel, Nicolas Leulliot, Marc Graille, Dominique Liger, Lionel Trésaugues, Joel L Sussman, Joël Janin, Herman van Tilbeurgh, Anne Poupon.   

Abstract

Structural genomics aims at the establishment of a universal protein-fold dictionary through systematic structure determination either by NMR or X-ray crystallography. In order to catch up with the explosive amount of protein sequence data, the structural biology laboratories are spurred to increase the speed of the structure-determination process. To achieve this goal, high-throughput robotic approaches are increasingly used in all the steps leading from cloning to data collection and even structure interpretation is becoming more and more automatic. The progress made in these areas has begun to have a significant impact on the more 'classical' structural biology laboratories, dramatically increasing the number of individual experiments. This automation creates the need for efficient data management. Here, a new piece of software, HalX, designed as an 'electronic lab book' that aims at (i) storage and (ii) easy access and use of all experimental data is presented. This should lead to much improved management and tracking of structural genomics experimental data.

Entities:  

Mesh:

Year:  2005        PMID: 15930618     DOI: 10.1107/S0907444905001290

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  12 in total

1.  Automation in biological crystallization.

Authors:  Patrick Shaw Stewart; Jochen Mueller-Dieckmann
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2014-05-28       Impact factor: 1.056

2.  Recording information on protein complexes in an information management system.

Authors:  Marc Savitsky; Jonathan M Diprose; Chris Morris; Susanne L Griffiths; Edward Daniel; Bill Lin; Susan Daenke; Benjamin Bishop; Christian Siebold; Keith S Wilson; Richard Blake; David I Stuart; Robert M Esnouf
Journal:  J Struct Biol       Date:  2011-05-14       Impact factor: 2.867

Review 3.  Biomarkers in autism spectrum disorder: the old and the new.

Authors:  Barbara Ruggeri; Ugis Sarkans; Gunter Schumann; Antonio M Persico
Journal:  Psychopharmacology (Berl)       Date:  2013-10-06       Impact factor: 4.530

4.  Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies.

Authors:  Damien Farrell; Fergal O'Meara; Michael Johnston; John Bradley; Chresten R Søndergaard; Nikolaj Georgi; Helen Webb; Barbara Mary Tynan-Connolly; Una Bjarnadottir; Tommy Carstensen; Jens Erik Nielsen
Journal:  Nucleic Acids Res       Date:  2010-08-19       Impact factor: 16.971

5.  Data management in the modern structural biology and biomedical research environment.

Authors:  Matthew D Zimmerman; Marek Grabowski; Marcin J Domagalski; Elizabeth M Maclean; Maksymilian Chruszcz; Wladek Minor
Journal:  Methods Mol Biol       Date:  2014

6.  People and organizational issues in research systems implementation.

Authors:  Joan S Ash; Nicholas R Anderson; Peter Tarczy-Hornoch
Journal:  J Am Med Inform Assoc       Date:  2008-02-28       Impact factor: 4.497

Review 7.  Benefits of structural genomics for drug discovery research.

Authors:  Marek Grabowski; Maksymilian Chruszcz; Matthew D Zimmerman; Olga Kirillova; Wladek Minor
Journal:  Infect Disord Drug Targets       Date:  2009-11

Review 8.  State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments.

Authors:  David R Cooper; Marek Grabowski; Matthew D Zimmerman; Przemyslaw J Porebski; Ivan G Shabalin; Magdalena Woinska; Marcin J Domagalski; Heping Zheng; Piotr Sroka; Marcin Cymborowski; Mateusz P Czub; Ewa Niedzialkowska; Barat S Venkataramany; Tomasz Osinski; Zbigniew Fratczak; Jacek Bajor; Juliusz Gonera; Elizabeth MacLean; Kamila Wojciechowska; Krzysztof Konina; Wojciech Wajerowicz; Maksymilian Chruszcz; Wladek Minor
Journal:  Methods Mol Biol       Date:  2021

9.  The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

Authors:  Chris Morris; Anne Pajon; Susanne L Griffiths; Ed Daniel; Marc Savitsky; Bill Lin; Jonathan M Diprose; Alan Wilter da Silva; Katya Pilicheva; Peter Troshin; Johannes van Niekerk; Neil Isaacs; James Naismith; Colin Nave; Richard Blake; Keith S Wilson; David I Stuart; Kim Henrick; Robert M Esnouf
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

10.  E-MSD: improving data deposition and structure quality.

Authors:  M Tagari; J Tate; G J Swaminathan; R Newman; A Naim; W Vranken; A Kapopoulou; A Hussain; J Fillon; K Henrick; S Velankar
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.