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GIB specifications


Unique identifier OMICS_19964
Name GIB
Alternative names Genome Information Broker for Viruses, GIB-V
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

Publication for Genome Information Broker for Viruses

GIB citations


Determining the minimum number of protein protein interactions required to support known protein complexes

PLoS One
PMCID: 5919440
PMID: 29698482
DOI: 10.1371/journal.pone.0195545

[…] LEX. All experiments were performed on a PC with Intel Core i7-2600 CPU (3.40 GHz) with 7.7 GB RAM running under the Fedora 21 with Linux kernel 3.14.2 and with Xeon E5-2667 CPU (3.30GHz×8) with 62.9 GiB memory running under the Mint 17.1 Cinnamon with Linux kernel 3.13.0-37-generic. We used the same CPU to compare the CPU time in each experiment. ILPMinPPI can be freely downloaded from http://sun […]


Neuromodulated Synaptic Plasticity on the SpiNNaker Neuromorphic System

Front Neurosci
PMCID: 5835099
PMID: 29535600
DOI: 10.3389/fnins.2018.00105

[…] evice of this type is the Jetson TX1, an embedded system with a peak power usage of only 18 W, yet still equipped with a 256 CUDA core “Maxwell” GPU as well as a 64 bit quad-core ARM Cortex-A57 and 4 GiB of LPDDR4 memory. Similarly to other GPU devices, the NVIDIA Jetson TX1 can be programmed using the Compute Unified Device Architecture (CUDA), meaning that a wealth of scientific software can be […]


Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease

NPJ Syst Biol Appl
PMCID: 5765040
PMID: 29354285
DOI: 10.1038/s41540-017-0044-x

[…] rg). The software makes use of Pyomo, to build the optimization problems and Gurobi and CPLEX to solve them.The performance of FNs remained within reasonable limits of CPU time (Intel i7, 2.00 GHz, 8 GiB, Ubuntu 14.04 LTS). Namely, the CPU time to compute one step in the glucose consumption model was 5.96 s for the wild-type cell and 44.36 s for the mutant with the state space partitioned in four […]


Analysis of the whole transcriptome from gingivo buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy

PLoS One
PMCID: 5590820
PMID: 28886030
DOI: 10.1371/journal.pone.0183606

[…] ses and integration sites, was applied to identify patients with or without infection of any virus such as HBV, HCV, HIV including HPV16 and HPV18. The VirusSeq uses a catalogue of 26512 viruses from GIB-V (genome information broker for viruses) database and check for their presence and integration sites in paired-end RNAseq data given to it. It uses a subtraction based method similar to PATHSeq. […]


Comparative proteomic analysis of Gib2 validating its adaptor function in Cryptococcus neoformans

PLoS One
PMCID: 5501510
PMID: 28686685
DOI: 10.1371/journal.pone.0180243

[…] Total RNA was extracted from the wild type H99 and the gib2 mutant strains that were subject to the same induction condition as for protein extraction, using the Trizol reagent (Invitrogen, CA). Following digestion with RNase-free DNase (RQ1, Promega), RN […]


A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data

PLoS One
PMCID: 5148592
PMID: 27936191
DOI: 10.1371/journal.pone.0168004

[…] the instance model “r3.2xlarge”, which is one of the “Memory Optimized Instances” offered by the service. Each node has 8 virtual High Frequency Intel Xeon E5-2670 v2 Ivy Bridge 2.5GHz Processors, 61 GiB of RAM and one SSD disk, 160 GB in sizeFor the test, we configured Apache Hadoop YARN and HDFS to run on twelve nodes. Ten nodes are configured as workers, while two are used as head nodes running […]


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GIB institution(s)
Center for Information Biology and DNA Data Bank of Japan National Institute of Genetics and Sokendai, Shizuoka, Japan; Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan; Life Science Systems Division, Fujitsu Limited, Tokyo, Japan
GIB funding source(s)
Supported by the Institute for Bioinformatics Research and Development of Japan Science and Technology Agency.

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