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Citations per year

Number of citations per year for the bioinformatics software tool MetaSpace
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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

Download


github.png

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


download.png

Versioning


No version available

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 citations

 (6)
library_books

Fourier Transform Infrared Microscopy Enables Guidance of Automated Mass Spectrometry Imaging to Predefined Tissue Morphologies

2018
Sci Rep
PMCID: 5762902
PMID: 29321555
DOI: 10.1038/s41598-017-18477-6

[…] 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 on […]

library_books

The impact of self avatars on trust and collaboration in shared virtual environments

2017
PLoS One
PMCID: 5730128
PMID: 29240837
DOI: 10.1371/journal.pone.0189078

[…] t, 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 for each user, […]

library_books

3D MALDI Mass Spectrometry Imaging of a Single Cell: Spatial Mapping of Lipids in the Embryonic Development of Zebrafish

2017
Sci Rep
PMCID: 5668422
PMID: 29097697
DOI: 10.1038/s41598-017-14949-x

[…] ed by separate MS/MS measurements for lipids (Supplementary Fig.  and Table ). Additionally, in order to assign a degree of confidence to the assignments, molecular annotation was performed using the METASPACE annotation engine. Results are publically available at annotate.metaspace2020.eu and are shown in Table .The video animations (Supplementary Videos ) of the 3D distributions of PE (22:6_16:0 […]

library_books

MHC2MIL: a novel multiple instance learning based method for MHC II peptide binding prediction by considering peptide flanking region and residue positions

2014
BMC Genomics
PMCID: 4290625
PMID: 25521198
DOI: 10.1186/1471-2164-15-S9-S9

[…] ed methods, where short substrings of varying sizes are used to measure the similarity between two peptides. MHC2MIL resorts to multiple instance learning techniques to map each peptide into a common metaspace. It is obvious that these methods are complement to each other, so that ensemble techniques could be used to further enhance the prediction performance [,]. […]

library_books

Integration of High Volume Molecular and Imaging Data for Composite Biomarker Discovery in the Study of Melanoma

2014
Biomed Res Int
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 differences […]

library_books

Supervised Regularized Canonical Correlation Analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery

2011
BMC Bioinformatics
PMCID: 3267835
PMID: 22182303
DOI: 10.1186/1471-2105-12-483

[…] In an ideal metaspace representation, samples from each class will be grouped together while the samples from different classes will be grouped separately. The WLT [] capitalizes on this knowledge and calculates […]


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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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