MetaSpace specifications

Information


Unique identifier OMICS_27289
Name MetaSpace
Alternative name pySM
Interface Web user interface
Restrictions to use None
Input data A high-resolution imaging mass spectrometry dataset.
Input format imzML
Computer skills Basic
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Andrew Palmer <>
  • person_outline Theodore Alexandrov <>
  • person_outline Team MetaSpace <>

Additional information


https://www.slideshare.net/Metaspace2020/metaspace-training-course-ourcon-v-2017

Information


Unique identifier OMICS_27289
Name MetaSpace
Alternative name pySM
Software type Application/Script, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A high-resolution mass spectrometry imaging dataset; a metabolite database and a configuration file.
Input format imzML+CSV
Operating system Unix/Linux, Mac OS
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Requirements
git, wget, unzip
Maintained Yes

Download


Versioning


Add your version

Maintainers


  • person_outline Andrew Palmer <>
  • person_outline Theodore Alexandrov <>
  • person_outline Team MetaSpace <>

Additional information


https://www.slideshare.net/Metaspace2020/metaspace-training-course-ourcon-v-2017

Publication for MetaSpace

MetaSpace in publications

 (4)
PMCID: 5762902
PMID: 29321555
DOI: 10.1038/s41598-017-18477-6

[…] image x and the fixed binary image y originating from the optical image used for msi acquisition., fticr datasets generated during and/or analyzed during the current study are available in the eu-metaspace repository [http://metaspace2020.eu/]. other datasets generated during and/or analyzed during the current study are not publicly available but are available from the corresponding author […]

PMCID: 5730128
PMID: 29240837
DOI: 10.1371/journal.pone.0189078

[…] easily configurable sve systems and applications have been developed. for example, muvr [] used a oculus rift hmd and a razer hydra tracking system, and created multiuser virtual reality platform. metaspace [] included a self-avatar by tracking each user’s body with a kinect device., inspired by these recently developed systems, we developed an sve system and provided a self-avatar […]

PMCID: 5670129
PMID: 29101330
DOI: 10.1038/s41598-017-14092-7

[…] with regard to jurisdictional claims in published maps and institutional affiliations., we acknowledge the financial support for bioinformatics developments as part of bbsrc (bb/l020858/1) and eu-metaspace (634402) projects; and imperial college stratified medicine graduate training programme in systems medicine and spectroscopic profiling (stratigrad). k. a. v. gratefully acknowledges […]

PMCID: 3914284
PMID: 24527435
DOI: 10.1155/2014/145243

[…] in a decision-fusion technique combining heterogeneous breast cancer data. lee et al. [] proposed a generalized fusion framework (gff) for homogenous data representation and subsequent fusion in the metaspace, using dimensionality reduction techniques. the metaspace comprises the projections of the heterogeneous data streams transformed in a way that scale and alleviate dimensionality […]


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MetaSpace institution(s)
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Center for Industrial Mathematics, University of Bremen, Bremen, Germany; Protim, Inserm U1085, IRSET, Rennes, France; Université de Rennes I, Rennes, France; Bruker Daltonik GmbH, Bremen, Germany; National Research University Higher School of Economics, St. Petersburg, Russia; Higher Institute of Information Technologies and Information Systems, Kazan Federal University, Kazan, Russia; SCiLS GmbH, Bremen, Germany; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
MetaSpace funding source(s)
Supported by the European Union’s Horizon2020 and FP7 programs under grant agreements 634402 and 305259 and from the Russian Government Program of Competitive Growth of Kazan Federal University.

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