| # 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 |
| <div itemscope itemtype="https://schema.org/Person"><a itemprop="sameAs" content="https://orcid.org/0000-0002-7364-0741" href="https://orcid.org/0000-0002-7364-0741" target="orcid.widget" rel="me noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">https://orcid.org/0000-0002-7364-0741</a></div> |
| |
| WeChat public account: Chemocoder |
| <img align="center" src="https://github.com/hcji/hcji/blob/main/img/qrcode.jpg" width="20%"/> |
| |
