Evidence map›Paper›PMID 25159034›Full record

ArticleBMC bioinformatics2014

MendeLIMS: a web-based laboratory information management system for clinical genome sequencing.

Susan M Grimes, Hanlee P Ji

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Susan M Grimes
Hanlee P JiStanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA. genomics_ji@stanford.edu.

Funding

WHOLE YEAST GENOME TRANSCRIPTIONAL AND FUNCTIONAL GENE MAPS--A FEASIBILITY STUDYP01HG000205 · NHGRI · STANFORD UNIVERSITY · PI DAVIS, RONALD WAYNE, HOWE, ROGER THOMAS · 1990 to 2016
$120.9M
Proteomics/GenomicsP30DK056339 · NIDDK · STANFORD UNIVERSITY · PI GREENBERG, HARRY BERNARD · 2001 to 2010
$10.4M
A Strategy for High Quality Clinical Resequencing of the Human GenomeRC2HG005570 · NHGRI · STANFORD UNIVERSITY · PI DAVIS, RONALD WAYNE · 2009 to 2010
$2.8M
Howard Hughes Medical InstituteNHGRI NIH HHS 2P01HG000205NHGRI NIH HHS P01 HG000205NHGRI NIH HHS RC2 HG005570NHGRI NIH HHS RC2HG005570NIDDK NIH HHS DK56339NIDDK NIH HHS P30 DK056339
6 · The paper itself

Abstract

backgroundLarge clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis.

resultsTo meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies.

conclusionsWe maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/.

Indexed as

Clinical Laboratory TechniquesInternetSoftwareDatabases, GeneticGene LibraryGenetic TestingGenomicsHealth Information ManagementHigh-Throughput Nucleotide SequencingHumansMedical InformaticsSequence Analysis, DNAUser-Computer Interface

Identifiers

PMID25159034
PMCPMC4155081

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.