Abstract:
BACKGROUND:Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. RESULTS:We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. CONCLUSIONS:Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Tan TW,Xie C,De Silva M,Lim KS,Patro CP,Lim SJ,Govindarajan KR,Tong JC,Choo KH,Ranganathan S,Khan AMdoi
10.1186/1471-2164-14-S5-S13subject
Has Abstractpub_date
2013-01-01 00:00:00pages
S13issn
1471-2164pii
1471-2164-14-S5-S13journal_volume
14 Suppl 5pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on trans...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6244-6
更新日期:2019-11-14 00:00:00
abstract:BACKGROUND:NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further invest...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-313
更新日期:2009-07-15 00:00:00
abstract:BACKGROUND:Hemolymph plays key roles in honey bee molecule transport, immune defense, and in monitoring the physiological condition. There is a lack of knowledge regarding how the proteome achieves these biological missions for both the western and eastern honey bees (Apis mellifera and Apis cerana). A time-resolved pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-563
更新日期:2014-07-05 00:00:00
abstract:BACKGROUND:Colon cancer occurrence is increasing worldwide, making it the third most frequent cancer. Although many therapeutic options are available and quite efficient at the early stages, survival is strongly decreased when the disease has spread to other organs. The identification of molecular markers of colon canc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4139-y
更新日期:2017-09-30 00:00:00
abstract:BACKGROUND:Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the famil...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1846-0
更新日期:2015-08-27 00:00:00
abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-271
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candid...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-624
更新日期:2013-09-16 00:00:00
abstract:BACKGROUND:Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S6-S14
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6221-0
更新日期:2019-11-15 00:00:00
abstract:BACKGROUND:The disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-266
更新日期:2010-04-27 00:00:00
abstract:BACKGROUND:The Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) is an enzyme involved in pivotal metabolic processes and in the mitochondrial dysfunction seen in the Alzheimer's disease. Here we use comparative genomic analyses to study the evolution of the HADH2 gene encodin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-202
更新日期:2006-08-09 00:00:00
abstract:BACKGROUND:Despite its primary economic importance, genomic information on olive tree is still lacking. 454 pyrosequencing was used to enrich the very few sequence data currently available for the Olea europaea species and to identify genes involved in expression of fruit quality traits. RESULTS:Fruits of Coratina, a ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-399
更新日期:2009-08-26 00:00:00
abstract:BACKGROUND:Nucleosome positioning has an important role in gene regulation. However, dynamic positioning in vivo casts doubt on the reliability of predictions based on DNA sequence characteristics. What role does sequence-dependent positioning play? In this paper, using a curvature profile model, nucleosomes are predic...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-72
更新日期:2011-01-27 00:00:00
abstract:BACKGROUND:Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-287
更新日期:2011-06-02 00:00:00
abstract:BACKGROUND:Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4567-3
更新日期:2018-03-02 00:00:00
abstract:BACKGROUND:It is believed that the main factors of low prenatal growth in mammals are genetic and environmental. We used isogenic mice maintained in standard conditions to analyze how natural non-genetic microsomia (low birth weight) is produced in inbred mice and its long term effect on health. To better understand th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-327
更新日期:2014-05-01 00:00:00
abstract:BACKGROUND:The occurrence of liver cancer is higher in males than in females, and the incidence increases during aging. Signaling pathways regulated by retinoid x receptor alpha (RXRalpha) are involved in hepatocellular carcinogenesis. The phenotype of hepatocyte RXRalpha deficient mice is different between genders. To...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-403
更新日期:2008-08-28 00:00:00
abstract:BACKGROUND:The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal mode...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-190
更新日期:2007-06-25 00:00:00
abstract:BACKGROUND:Mytilisepta virgata is a marine mussel commonly found along the coasts of Japan. Although this species has been the subject of occasional studies concerning its ecological role, growth and reproduction, it has been so far almost completely neglected from a genetic and molecular point of view. In the present ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4012-z
更新日期:2017-08-08 00:00:00
abstract:BACKGROUND:The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting st...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-82
更新日期:2012-02-29 00:00:00
abstract:BACKGROUND:The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-152
更新日期:2011-03-16 00:00:00
abstract:BACKGROUND:The cotton (Gossypium spp.) fiber cell is an important unicellular model for studying cell differentiation. There is evidence suggesting that phosphorylation is a critical post-translational modification involved in regulation of a wide range of cell activities. Nevertheless, the sites of phosphorylation in ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-466
更新日期:2014-06-12 00:00:00
abstract:BACKGROUND:Celiac disease (CD) is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes) that mediate the stimulation of HL...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-277
更新日期:2012-06-22 00:00:00
abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-630
更新日期:2014-07-28 00:00:00
abstract:BACKGROUND:Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses. RESULTS:Here, we systematically assessed the utility of paired-end and mat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-257
更新日期:2013-04-16 00:00:00
abstract:BACKGROUND:Filarial nematodes cause debilitating human diseases. While treatable, recent evidence suggests drug resistance is developing, necessitating the development of novel targets and new treatment options. Although transcriptomic and proteomic studies around the nematode life cycle have greatly enhanced our knowl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2083-2
更新日期:2015-11-11 00:00:00
abstract:BACKGROUND:Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs), the materials ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-346
更新日期:2012-07-28 00:00:00
abstract:BACKGROUND:Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning ef...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-92
更新日期:2005-06-14 00:00:00
abstract:BACKGROUND:Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elemen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3693-7
更新日期:2017-04-20 00:00:00
abstract:BACKGROUND:Due to the high morbidity and mortality of fulminant hepatitis, early diagnosis followed by early effective treatment is the key for prognosis improvement. So far, little is known about the gene expression changes in the early stage of this serious illness. Identification of the genes related to the very ear...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-240
更新日期:2010-04-15 00:00:00