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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 |
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Maintainers
- person_outline Andrew Palmer
- person_outline Theodore Alexandrov
- person_outline Team MetaSpace
Additional information
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 |
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Versioning
No version available
Maintainers
- person_outline Andrew Palmer
- person_outline Theodore Alexandrov
- person_outline Team MetaSpace
Additional information
Publication for MetaSpace
MetaSpace citations
(6)Fourier Transform Infrared Microscopy Enables Guidance of Automated Mass Spectrometry Imaging to Predefined Tissue Morphologies
[…] 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 […]
The impact of self avatars on trust and collaboration in shared virtual environments
[…] 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, […]
3D MALDI Mass Spectrometry Imaging of a Single Cell: Spatial Mapping of Lipids in the Embryonic Development of Zebrafish
[…] 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 […]
MHC2MIL: a novel multiple instance learning based method for MHC II peptide binding prediction by considering peptide flanking region and residue positions
[…] 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 [,]. […]
Integration of High Volume Molecular and Imaging Data for Composite Biomarker Discovery in the Study of Melanoma
[…] 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 […]
Supervised Regularized Canonical Correlation Analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery
[…] 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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