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CellBase specifications


Unique identifier OMICS_14259
Name CellBase
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 4.0.0
Stability Stable
Perl, Ensembl API, MongoDB, Tomcat
Maintained Yes




No version available



  • person_outline Ignacio Medina <>

Publication for CellBase

CellBase citations


Recent advances in predicting gene–disease associations

PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] data sources are constantly updated. one would need to determine whether the different components are using the same database version. a solution would be to use third-party data providers such as cellbase , which provides web services for retrieving biological information from heterogeneous sources to handle data harmonisation across different tools., unconventional approaches […]


The pan cancer pathological regulatory landscape

PMCID: 5175166
PMID: 28000771
DOI: 10.1038/srep39709

[…] tfbss within the chip-seq peaks (details can be found in specific ensembl web pages). this information is accessible in a more efficient way in different publicly available resources, such as cellbase, whose web services were used here. shows the list of target genes for each tf., since direct inference of tf activity from its own gene expression level is problematic, in this work […]


Identification of epistatic interactions through genome wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas

PMCID: 4685628
PMID: 26690675
DOI: 10.1186/s12920-015-0160-7

[…] localization was taken from the human protein atlas [] and the geo repository []. finally, information about non-coding rnas was obtained from nextprot [], noncode v4.0 [] and ensembl through the cellbase application []., after the quality control process, a total of 158 samples in the smtc vs control dataset (49 smtc and 109 control with 639,289 snps) and 149 samples in the ptc vs control […]


Long Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array

PMCID: 3977849
PMID: 24710337
DOI: 10.1371/journal.pone.0093466

[…] or tracking. cells are introduced by simple flow loading, devices are readily available from microfluidic foundries (caltech, stanford), and device schematics and software tools are available at cellbase.epfl.ch., we designed a microfluidic device consisting of 120 microchemostat growth chambers based on a design previously applied to large-scale single cell studies in s. cerevisiae () . […]


Whole genome bisulfite DNA sequencing of a DNMT3B mutant patient

PMCID: 3398983
PMID: 22595875
DOI: 10.4161/epi.20523

[…] (illumina)., we perform the sequences alignment and methylation calling with version 2.43 of bsmap software. all genomic information, unless otherwise expressly stated, was obtained using cellbase. sam/bam and bed files handling was done using samtools and bedtools. statistical analysis and graphic representation was performed with r (http://www.r-project.org) and libraries multicore […]


Automation of large scale transient protein expression in mammalian cells

PMCID: 3477309
PMID: 21571074
DOI: 10.1016/j.jsb.2011.04.017

[…] were detached using trypsin–edta (sigma), seeded in a t75 flask (corning or greiner) and finally transferred to a barcoded t175 flask (corning or bd-falcon) and imported into the compact select cellbase robot (the automation partnership, royston, uk), where all subsequent cell maintenance was automated., cells were harvested from 90% confluent t175 flasks, analysed by the cedex automated […]

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CellBase institution(s)
Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain; CIBER de Enfermedades Raras, Valencia, Spain; Functional Genomics Node (INB) at CIPF, Valencia, Spain; Research Center on Software Production Methods (ProS). DSIC Universitat Politècnica de València (UPV), Valencia, Spain
CellBase funding source(s)
The Spanish Ministry of Science and Innovation (MICINN) [BIO2011-27069]; the Conselleria de Educacio of the Valencian Community [PROMETEO/2010/001]; National Institute of Bioinformatics (www.inab.org); CIBER de Enfermedades Raras (CIBERER), ISCIII and MICINN; Red Tematica de Investigacion Cooperativa en Cancer (RTICC) [RD06/0020/1019] ISCIII, MICINN and INNPACTO [IPT-010000-2010-43], MICINN.

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