BASE statistics

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Associated diseases

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BASE specifications

Information


Unique identifier OMICS_00749
Name BASE
Alternative name BioArray Software Environment
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.11.2
Stability Stable
Requirements
Apache Tomcat servlet container, MySQL/PostgreSQL
Source code URL http://base.thep.lu.se/chrome/site/files/base/base-3.11.2-src.tar.gz
Maintained Yes

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Maintainers


  • person_outline Jari Häkkinen <>
  • person_outline Johan Vallon-Christersson <>
  • person_outline Nicklas Nordborg <>
  • person_outline Martin Svensson <>

Additional information


A demo is available as a web application: https://base.onk.lu.se/demo/ http://base.thep.lu.se/chrome/site/latest/html/index.html

Information


Unique identifier OMICS_00749
Name BASE
Alternative name BioArray Software Environment
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.10.0
Stability Stable
Registration required Yes
Maintained Yes

Maintainers


  • person_outline Jari Häkkinen <>
  • person_outline Johan Vallon-Christersson <>
  • person_outline Nicklas Nordborg <>
  • person_outline Martin Svensson <>

Additional information


A demo is available as a web application: https://base.onk.lu.se/demo/ http://base.thep.lu.se/chrome/site/latest/html/index.html

Publications for BioArray Software Environment

BASE in publications

 (55)
PMCID: 5817401
PMID: 29341157
DOI: 10.1002/bjs.10741

[…] patient's documents. all written informed consent forms are sent to the project coordinator, who also deals with retraction of consent. a customized laboratory information management system (lims), bioarray software environment (base), has also been established to enable description of the representativeness of the population‐based sample, as well as routines for the retraction of informed […]

PMCID: 5549301
PMID: 28789624
DOI: 10.1186/s12885-017-3524-x

[…] p < 0.05 was considered statistically significant., in the transcriptional analysis, data pre-processing and quantile normalization were performed on the raw signal intensities using the web-based bioarray software environment (base) system. differentially expressed transcripts (between experimental groups) were identified using nexus expression 3.0 (biodiscovery, el segundo, ca, usa) as previo […]

PMCID: 5241264
PMID: 28097640
DOI: 10.1186/s13550-016-0247-y

[…] beadchips were analyzed using the illumina iscan n240 microarray scanner (illumina, ca, usa). data pre-processing and quantile normalization were performed on the raw signal intensities using the bioarray software environment (base) system. further processing was then performed using nexus expression 3.0 (biodiscovery, ca, usa) as previously described [, ]. the gene ontology (go) database […]

PMCID: 5214746
PMID: 28070562
DOI: 10.1128/mSphere.00291-16

[…] scanning, and analysis using the cyber-t web interface were performed as described previously (). data were normalized without background subtraction by the global lowess method using base (bioarray software environment; http://base.thep.lu.se/), excluding empty wells and arabidopsis thaliana control spots., the genes of interest were amplified from s. pneumoniae d39 genomic dna using […]

PMCID: 5312337
PMID: 27458152
DOI: 10.18632/oncotarget.10746

[…] 3 data for the 661 tumors included in this analysis were processed as previously described []., microarray data were pre-processed and quantile-normalized using the genomestudio software v2011.1 and bioarray software environment (base) v3.4.1 respectively. probe sets with signal intensities below the median of the negative control intensity signals in ≥80% of the samples were excluded. […]


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BASE institution(s)
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden; CREATE Health Strategic Centre for Translational Cancer Research, Lund University, Lund, Sweden; Department of Theoretical Physics, Lund University, Lund, Sweden

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