File size: 2,860 Bytes
fb5f46a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 | # DeepMASS2
DeepMASS2 is a cross-platform GUI software tool, which enables deep-learning based metabolite annotation
via semantic similarity analysis of mass spectral language. This approach enables the prediction
of structurally related metabolites for the unknown compounds. By considering the chemical space, these
structurally related metabolites provide valuable information about the potential location of the unknown
metabolites and assist in ranking candidates obtained from molecular structure databases.
## Installation
Please follow the following installation steps:
1. Install [Anaconda](https://www.anaconda.com/) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
2. Create a new conda environment and activate:
conda create -n deepmass python=3.8.13
conda activate deepmass
3. Clone the repository and enter:
git clone https://github.com/hcji/DeepMASS2_GUI.git
cd DeepMASS2_GUI
4. Install dependency (note, for *MacOS* some dependency may install with conda manually):
pip install -r requirements.txt
5. Download the [dependent data](https://github.com/hcji/DeepMASS2_GUI/releases/tag/v0.99.0).
1) put the following files into *data* folder:
DeepMassStructureDB-v1.0.csv
references_index_negative_spec2vec.bin
references_index_positive_spec2vec.bin
references_spectrums_negative.pickle
references_spectrums_positive.pickle
2) put the following files into *model* folder:
Ms2Vec_allGNPSnegative.hdf5
Ms2Vec_allGNPSnegative.hdf5.syn1neg.npy
Ms2Vec_allGNPSnegative.hdf5.wv.vectors.npy
Ms2Vec_allGNPSpositive.hdf5
Ms2Vec_allGNPSpositive.hdf5.syn1neg.npy
Ms2Vec_allGNPSpositive.hdf5.wv.vectors.npy
6. Run DeepMASS
python DeepMASS2.py
## Release
* [Version 0.99.0](https://github.com/hcji/DeepMASS2_GUI/releases/tag/v0.99.0)
## Documentation
For the details on how to use DeepMASS, please check [Ducomentation](https://github.com/hcji/DeepMASS2_GUI/blob/main/document/documentation.md).
## Citation
In preparation
## Contact
Ji Hongchao
E-mail: ji.hongchao@foxmail.com
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