https://sourceforge.net/p/novoglycox/wiki/Home/Recent changes to HomeenSat, 30 May 2026 11:08:58 -0000https://sourceforge.net/p/novoglycox/wiki/Home/<div class="markdown_content"><pre>--- v5 +++ v6 @@ -7,6 +7,8 @@ NovoGlyco works in tandem with [Oxonium Browser](https://sourceforge.net/projects/oxoniumbrowserx/) for discovering diagnostic sugar oxonium ions in MS/MS data. The platform is designed for prokaryotic systems where glycan compositions are often novel or poorly characterised, traditional database search approaches fail due to unknown modifications. + +Available as a standalone executable, a Docker version, and Python source code at SourceForge: https://sourceforge.net/projects/novoglycox/files/ ## How It Works @@ -49,14 +51,7 @@ ## Getting Started -For installation instructions, input file requirements, Docker commands, and parameter configuration, see the [README](https://sourceforge.net/p/novoglycox/wiki/README/) on the project files page. - -For a quick overview: - -1. Place your `.mzML`, `.fasta`, and oxonium `.xlsx` files in the `Input/` folder -2. Build and run the Docker container -3. Access the dashboard at `http://localhost:8050` -4. Click mass delta bins to explore glycoprotein candidates +For the Python and Docker versions, installation instructions, input file requirements, Docker commands, and parameter configuration are described in the README files included in the respective ZIP packages. No installation is required for the standalone executable. ## Wiki Pages </pre> </div>glycolabSat, 30 May 2026 11:08:58 -0000https://sourceforge.nete49a51ea25a8e4438394e0c494edfd112d8ea974https://sourceforge.net/p/novoglycox/wiki/Home/<div class="markdown_content"><pre>--- v4 +++ v5 @@ -12,13 +12,13 @@ ``` ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ -│ Input Files │────▶│ SAGE Database │───▶│ Spectral │────▶│ Oxonium Ion │ +│ Input Files │───▶│ SAGE Database │────▶│ Spectral │───▶│ Oxonium Ion │ │ Processing │ │ Search │ │ Processing │ │ Annotation │ └───────────────┘ └───────────────┘ └───────────────┘ └───────────────┘ │ ▼ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ -│ Interactive │◀────│ Glycopeptide │◀───│ Sequence Tag │◀───│ DirectTag De │ +│ Interactive │◀────│ Glycopeptide │◀───│ Sequence Tag │◀───│ DirectTag De │ │ Dashboard │ │ Validation │ │ Matching │ │Novo Sequencing│ └───────────────┘ └───────────────┘ └───────────────┘ └───────────────┘ ``` </pre> </div>Dinko SoicWed, 18 Mar 2026 15:15:42 -0000https://sourceforge.net87cceaf7c4444bd0796fe746711d9e9520f65a5ahttps://sourceforge.net/p/novoglycox/wiki/Home/<div class="markdown_content"><pre>--- v3 +++ v4 @@ -12,13 +12,13 @@ ``` ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ -│ Input Files │────▶│ SAGE Database │────▶│ Spectral │────▶│ Oxonium Ion │ +│ Input Files │────▶│ SAGE Database │───▶│ Spectral │────▶│ Oxonium Ion │ │ Processing │ │ Search │ │ Processing │ │ Annotation │ └───────────────┘ └───────────────┘ └───────────────┘ └───────────────┘ │ ▼ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ -│ Interactive │◀────│ Glycopeptide │◀────│ Sequence Tag │◀────│ DirectTag De │ +│ Interactive │◀────│ Glycopeptide │◀───│ Sequence Tag │◀───│ DirectTag De │ │ Dashboard │ │ Validation │ │ Matching │ │Novo Sequencing│ └───────────────┘ └───────────────┘ └───────────────┘ └───────────────┘ ``` </pre> </div>Dinko SoicFri, 13 Mar 2026 08:55:02 -0000https://sourceforge.netfc7a17dd4230a0a376186c930bbc1dad248943cchttps://sourceforge.net/p/novoglycox/wiki/Home/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -2,255 +2,78 @@ ## Overview -NovoGlyco is a glycoproteomics platform specifically designed for identifying and characterizing prokaryotic protein glycosylation from large-scale shotgun proteomics data. It combines traditional database searching, oxonium ion detection, de novo sequencing, and sequence-tag matching to provide a comprehensive solution for untargeted glycopeptide identification without prior knowledge of glycan compositions. -The platform is designed to handle the complex challenge of identifying glycopeptides in prokaryotic systems, where: +NovoGlyco is a fully untargeted glycoproteomics platform for identifying and characterizing prokaryotic protein glycosylation directly from shotgun proteomics data. NovoGlyco integrates de novo discovery of oxonium ions, sequence tag database matching, and mass offset binning to extract glycan mass, composition and attachment types. Results are provided with an interactive visualization framework that supports exploration of glycan features and glycoproteins. -The platform is designed to handle the complex challenge of identifying glycopeptides in prokaryotic systems, where: -- Glycan compositions are often novel or poorly characterized -- Traditional database search approaches fail due to unknown modifications -- Glycopeptide fragmentation can be challenging to interpret +NovoGlyco works in tandem with [Oxonium Browser](https://sourceforge.net/projects/oxoniumbrowserx/) for discovering diagnostic sugar oxonium ions in MS/MS data. -NovoGlyco addresses these challenges through a hybrid approach combining database search, oxonium ion detection, de novo sequencing, and sequence tag matching, all integrated within a containerized environment for reproducible analysis. +The platform is designed for prokaryotic systems where glycan compositions are often novel or poorly characterised, traditional database search approaches fail due to unknown modifications. + +## How It Works + +``` +┌───────────────┐ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ +│ Input Files │────▶│ SAGE Database │────▶│ Spectral │────▶│ Oxonium Ion │ +│ Processing │ │ Search │ │ Processing │ │ Annotation │ +└───────────────┘ └───────────────┘ └───────────────┘ └───────────────┘ + │ + ▼ +┌───────────────┐ ┌───────────────┐ ┌───────────────┐ ┌───────────────┐ +│ Interactive │◀────│ Glycopeptide │◀────│ Sequence Tag │◀────│ DirectTag De │ +│ Dashboard │ │ Validation │ │ Matching │ │Novo Sequencing│ +└───────────────┘ └───────────────┘ └───────────────┘ └───────────────┘ +``` + +The pipeline: + +1. **SAGE database search** identifies unmodified peptides and creates a focused protein database +2. **Spectral processing** decharges all unmatched MS2 spectra and calculates precursor offsets +3. **Oxonium ion annotation** flags which diagnostic sugar fragment ions are present per spectrum +4. **De novo sequencing** (DirecTag) generates sequence tags from all unmatched spectra +5. **Tag matching** identifies peptides via dictionary-based lookup, optionally validated by Y0 ion presence +6. **Mass delta and offset binning** reveals glycan masses and monosaccharide compositions +7. **Interactive dashboard** presents glycoprotein candidates with oxonium evidence for exploration ## Key Features -- **Integrated Glycopeptide Identification Pipeline** - - SAGE database search for unmodified peptide identification - - Oxonium ion screening for glycopeptide detection - - DirectTag de novo sequencing for partial peptide sequences - - Sequence-tag matching to proteome databases - -- **Glycan Analysis** - - Mass delta analysis for determining glycan mass - - Precursor and peptide offsets reveal glycan composition - - Oxonium ion co-occurrence analysis for reconstruction of the glycan +**Glycan Database-Independent Search** +All unmatched spectra undergo tag matching regardless of oxonium ion content, without requiring a predefined glycan database. This catches glycopeptides with novel or unexpected glycan compositions, including those where oxonium ions are absent or below threshold. Y0 ion validation is enabled by default for increased confidence but can be disabled to maximise sensitivity (see [Analysis Parameters](https://sourceforge.net/p/novoglycox/wiki/Analysis%20Parameters/)). The oxonium-filtered view is available as a confidence layer on top of the untargeted results. -- **Interactive Visualization** - - Web-based dashboard for exploring glycopeptide identifications - - Dynamic histogram visualization of mass distributions - - Comparative analysis of target vs. decoy matches +**Glycan Composition Analysis** +Three complementary mass metrics — mass deltas, precursor offsets, and peptide offsets — provide independent evidence for glycan mass and monosaccharide composition. Precursor offset analysis works even when peptide identification fails, enabling glycan exploration across all oxonium-positive spectra. See [Key Metrics](https://sourceforge.net/p/novoglycox/wiki/Key%20Metrics/) for details. -## Workflow +**Protein-Centric Dashboard** +An interactive Plotly Dash interface presents results as ranked glycoprotein candidates with collapsible peptide details. Each protein shows PSM count, unique peptides, median tag count, and oxonium evidence as coloured dots. Oxonium filter checkboxes allow progressive refinement from untargeted results to high-confidence glycopeptide candidates. See [Interactive Dashboard](https://sourceforge.net/p/novoglycox/wiki/Interactive%20Dashboard/) for a full guide. -1. **Initial database search identifies proteins using SAGE** - - Unmodified peptides are identified via database search - - Proteins and scan numbers from identified peptides are extracted +**Oxonium Ion Co-occurrence** +A heatmap reveals which monosaccharides co-occur on the same spectra, supporting glycan structure reconstruction directly from shotgun data. -2. **MS/MS spectra are filtered for oxonium ion presence** - - MS/MS spectra are screened for diagnostic sugar oxonium ions - - Scans already identified by SAGE are excluded - - HCD/ETD paired scans are identified for complementary analysis +## Getting Started -3. **De novo sequencing generates partial peptide tags** - - De novo sequence tags are generated from spectra - - De novo tags are filtered for oxonium-containing spectra +For installation instructions, input file requirements, Docker commands, and parameter configuration, see the [README](https://sourceforge.net/p/novoglycox/wiki/README/) on the project files page. -4. **Tags are used for identification of potential glycopeptides** - - Tags are matched against database peptides - - Peptide matches are validated by Y0 ion presence - - Results are grouped by peptide-protein combinations +For a quick overview: -5. **Binned mass offsets provide glycan mass and composition** - - Offsets are binned for pattern recognition - - Mass deltas indicate glycan mass - - Precursor/peptide offsets indicate glycan building blocks +1. Place your `.mzML`, `.fasta`, and oxonium `.xlsx` files in the `Input/` folder +2. Build and run the Docker container +3. Access the dashboard at `http://localhost:8050` +4. Click mass delta bins to explore glycoprotein candidates -6. **Interactive dashboard enables exploration of results** - - Oxonium ion co-occurrence is visualized as a heatmap - - Histogram instensity plots of binned offsets showcase glycan patterns - - Data tables provide detailed information on potential glycopeptides +## Wiki Pages -## System Requirements - -- [Docker](https://www.docker.com/get-started) (version 19.03 or higher recommended) -- At least 4GB of available RAM -- At least 10GB of free disk space -- For Astral raw files, increased memory will be required. - -## Quick Start - -1. Download and extract the project: - ```bash - # Download the latest release from SourceForge - # https://sourceforge.net/projects/novoglyco/files/ - - # Extract the downloaded archive - unzip novoglyco-docker-v1.0.0.zip - # or - tar -xzf novoglyco-docker-v1.0.0.tar.gz - - # Navigate to the project directory - cd novoglyco-docker - ``` - -2. Prepare your input files - - Place your `.mzML` files (MS/MS data), `.fasta` files (protein database), and `.xlsx` file (oxonium ion definitions) in the `Input` directory - - The DirectTag executable files are already included in the `directag_windows_64bits` directory for Windows and `directag_linux_64bit` directory for Linux - -3. Build the Docker image: - ```bash - docker build -t novoglyco . - ``` - -4. **Run NovoGlyco** using one of the following methods: - - First, ensure any previous NovoGlyco container is removed: - ```bash - docker rm -f novoglyco - ``` - - ### Option 1: Single Command (recommended for first-time runs) - - Run both DirectTag and Docker together with a single command: - - **For Windows (Command Prompt):** - ``` - start "DirectTag Process" cmd /c run_directag_windows.bat &amp; docker run --name novoglyco -p 8050:8050 -v "%cd%\Input:/app/Input" -v "%cd%\Output:/app/Output" novoglyco - ``` - - **For Windows (PowerShell):** - ``` - Start-Process -FilePath "cmd" -ArgumentList "/c run_directag_windows.bat"; docker run --name novoglyco -p 8050:8050 -v "${PWD}\Input:/app/Input" -v "${PWD}\Output:/app/Output" novoglyco - ``` - - **For Linux/macOS:** - ``` - ./run_directag_linux.sh &amp; docker run --name novoglyco -p 8050:8050 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" novoglyco - ``` - - ### Option 2: Separate Commands - - Run both processes in separate terminal windows: - - **Terminal 1 - Start DirectTag script:** - - For Windows: - ``` - run_directag_windows.bat - ``` - - For Linux: - ``` - ./run_directag_linux.sh - ``` - - **Terminal 2 - Start Docker container:** - - For Windows Command Prompt: - ``` - docker run --name novoglyco -p 8050:8050 -v "%cd%\Input:/app/Input" -v "%cd%\Output:/app/Output" novoglyco - ``` - - For PowerShell: - ``` - docker run --name novoglyco -p 8050:8050 -v "${PWD}\Input:/app/Input" -v "${PWD}\Output:/app/Output" novoglyco - ``` - - For Linux/macOS: - ``` - docker run --name novoglyco -p 8050:8050 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" novoglyco - ``` - - ### Option 3: Docker Only (when tags are already generated) - - If you already have DirectTag tags files in your Input directory with the desired tag length, you can skip the DirectTag execution and run only the Docker container: - - For Windows Command Prompt: - ``` - docker run --name novoglyco -p 8050:8050 -v "%cd%\Input:/app/Input" -v "%cd%\Output:/app/Output" novoglyco - ``` - - For PowerShell: - ``` - docker run --name novoglyco -p 8050:8050 -v "${PWD}\Input:/app/Input" -v "${PWD}\Output:/app/Output" novoglyco - ``` - - For Linux/macOS: - ``` - docker run --name novoglyco -p 8050:8050 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" novoglyco - ``` - - **Note:** For the Docker-only approach to work, there must be a tags file in the Input directory named exactly `[mzML_filename]_DIRECTAG_top10_tag[Tag_Length].tags`. If you've previously generated tags with a different naming convention, make sure to rename them accordingly. - - -5. Access the interactive dashboard - - Open your browser and navigate to: `http://localhost:8050` - -6. Results will be saved to the `Output` directory - -7. To analyze the next set of data or use different parameters: - - Press `Ctrl+C` to stop the current container (Note: This may not fully exit the container) - - Run `docker ps` to identify any containers still running: - ``` - docker ps - ``` - - Stop any running NovoGlyco containers: - ``` - docker stop [CONTAINER_ID] - ``` - or to stop all running containers: - ``` - docker stop $(docker ps -q) - ``` - - Replace the input files in the `Input` directory - - Run the Docker command again with desired parameters (see "Running with Custom Parameters" section) - NOTE: Output will be overwritten if the same input files are used - - -## License - -NovoGlyco is released under the Apache License 2.0. - -Copyright (c) 2025 - -Licensed under the Apache License, Version 2.0 (the "License"); -you may not use this software except in compliance with the License. -You may obtain a copy of the License at: - -http://www.apache.org/licenses/LICENSE-2.0 - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an "AS IS" BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -Please note that some of the functions and libraries used by NovoGlyco may not share the same license as NovoGlyco. -If you want to use any of these in a different context, ensure that you obtain the appropriate licenses for the dependent libraries and tools. -Additional info dependencies and functions (not complete): - -Python: Python 3.x, open-source, https://www.python.org/ -Dash: MIT License, https://dash.plotly.com/ -Pyteomics: MIT License, https://pyteomics.readthedocs.io/ -pandas: BSD 3-Clause License, https://pandas.pydata.org/ -matplotlib: Matplotlib is licensed under the PSF License, https://matplotlib.org/ -scipy: BSD 3-Clause License, https://scipy.org/ -numpy: BSD 3-Clause License, https://numpy.org/ -Sage: MIT License, https://github.com/lazear/sage (Used for advanced spectrum annotation and pre-filtering) -Lazear, Michael R. "Sage: an open-source tool for fast proteomics searching and quantification at scale." -Journal of Proteome Research 22.11 (2023): 3652-3659. -Other Python Libraries: Please review the licenses for any other third-party packages used. -Version/History: Version 1.0.0 - -Future versions will continue to improve functionality and performance, with regular updates to fix bugs and add features. - -Data/Privacy: -NovoGlyco does not collect, store, or transmit any personal data. It operates entirely on the local machine and does not interact with any external servers or services. All data processing and analysis occur locally, and the application does not send or receive any data over the internet unless specifically configured to do so (e.g., if the user chooses to share files for support purposes). -Data Collection: No data is collected by the Oxonium Explorer itself. However, any files processed using Oxonium Explorer (such as proteomics data files) are handled on the user's local machine and are not transmitted unless manually shared by the user. -Data Security: Oxonium Explorer does not store any sensitive data and does not have access to personal or confidential information. All data handling is kept within the scope of the users local environment, and files are not uploaded or shared without explicit user action. -Privacy Policy: Since Oxonium Explorer does not engage in data collection or sharing, a privacy policy is not required. However, users should ensure they are aware of the privacy policies of any external tools or libraries that may collect data in their respective functionalities. -User Consent: By using Oxonium Explorer, you consent to the software operating on your local machine as described above, and you are responsible for managing your own data and files. - -No Warranty Disclaimer: -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -Please ensure you are complying with the terms and conditions of the dependencies and their respective licenses. +| Page | Description | +|------|-------------| +| [Key Metrics](https://sourceforge.net/p/novoglycox/wiki/Key%20Metrics/) | Explanation of mass delta, precursor offsets, peptide offsets, tag counts, and other analytical metrics | +| [Interactive Dashboard](https://sourceforge.net/p/novoglycox/wiki/Interactive%20Dashboard/) | Guide to the dashboard visualisations, glycoprotein candidate table, oxonium filter, and Excel export | +| [Analysis Parameters](https://sourceforge.net/p/novoglycox/wiki/Analysis%20Parameters/) | Complete parameter reference with defaults, descriptions, and recommended combinations | +| [System Architecture](https://sourceforge.net/p/novoglycox/wiki/System%20Architecture/) | Technical documentation of the pipeline architecture, module descriptions, and data flow | ## Citation If you use this software in your research, please cite: -Soic D and Pabst M. NovoGlyco: mapping protein glycosylation in prokaryotes. bioRxiv. 2025. + +&gt; Šoić D. and Pabst M. NovoGlyco: mapping protein glycosylation in prokaryotes. bioRxiv. 2026. ## Contacts -Dinko Soic (dsoic@pharma.hr) +Dinko Šoić (soic@imsb.biol.ethz.ch) Martin Pabst (m.pabst@tudelft.nl) </pre> </div>Dinko SoicFri, 13 Mar 2026 08:54:10 -0000https://sourceforge.neta0b79dff15e2d9b2a45a40775395fd40c013deachttps://sourceforge.net/p/novoglycox/wiki/Home/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -1,8 +1,256 @@ -Welcome to your wiki! - -This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage]. - -The wiki uses [Markdown](/p/novoglycox/wiki/markdown_syntax/) syntax. - -[[members limit=20]] -[[download_button]] +# NovoGlyco: Comprehensive Glycoproteomics Platform + +## Overview + +NovoGlyco is a glycoproteomics platform specifically designed for identifying and characterizing prokaryotic protein glycosylation from large-scale shotgun proteomics data. It combines traditional database searching, oxonium ion detection, de novo sequencing, and sequence-tag matching to provide a comprehensive solution for untargeted glycopeptide identification without prior knowledge of glycan compositions. +The platform is designed to handle the complex challenge of identifying glycopeptides in prokaryotic systems, where: + +The platform is designed to handle the complex challenge of identifying glycopeptides in prokaryotic systems, where: +- Glycan compositions are often novel or poorly characterized +- Traditional database search approaches fail due to unknown modifications +- Glycopeptide fragmentation can be challenging to interpret + +NovoGlyco addresses these challenges through a hybrid approach combining database search, oxonium ion detection, de novo sequencing, and sequence tag matching, all integrated within a containerized environment for reproducible analysis. + +## Key Features + +- **Integrated Glycopeptide Identification Pipeline** + - SAGE database search for unmodified peptide identification + - Oxonium ion screening for glycopeptide detection + - DirectTag de novo sequencing for partial peptide sequences + - Sequence-tag matching to proteome databases + +- **Glycan Analysis** + - Mass delta analysis for determining glycan mass + - Precursor and peptide offsets reveal glycan composition + - Oxonium ion co-occurrence analysis for reconstruction of the glycan + +- **Interactive Visualization** + - Web-based dashboard for exploring glycopeptide identifications + - Dynamic histogram visualization of mass distributions + - Comparative analysis of target vs. decoy matches + +## Workflow + +1. **Initial database search identifies proteins using SAGE** + - Unmodified peptides are identified via database search + - Proteins and scan numbers from identified peptides are extracted + +2. **MS/MS spectra are filtered for oxonium ion presence** + - MS/MS spectra are screened for diagnostic sugar oxonium ions + - Scans already identified by SAGE are excluded + - HCD/ETD paired scans are identified for complementary analysis + +3. **De novo sequencing generates partial peptide tags** + - De novo sequence tags are generated from spectra + - De novo tags are filtered for oxonium-containing spectra + +4. **Tags are used for identification of potential glycopeptides** + - Tags are matched against database peptides + - Peptide matches are validated by Y0 ion presence + - Results are grouped by peptide-protein combinations + +5. **Binned mass offsets provide glycan mass and composition** + - Offsets are binned for pattern recognition + - Mass deltas indicate glycan mass + - Precursor/peptide offsets indicate glycan building blocks + +6. **Interactive dashboard enables exploration of results** + - Oxonium ion co-occurrence is visualized as a heatmap + - Histogram instensity plots of binned offsets showcase glycan patterns + - Data tables provide detailed information on potential glycopeptides + +## System Requirements + +- [Docker](https://www.docker.com/get-started) (version 19.03 or higher recommended) +- At least 4GB of available RAM +- At least 10GB of free disk space +- For Astral raw files, increased memory will be required. + +## Quick Start + +1. Download and extract the project: + ```bash + # Download the latest release from SourceForge + # https://sourceforge.net/projects/novoglyco/files/ + + # Extract the downloaded archive + unzip novoglyco-docker-v1.0.0.zip + # or + tar -xzf novoglyco-docker-v1.0.0.tar.gz + + # Navigate to the project directory + cd novoglyco-docker + ``` + +2. Prepare your input files + - Place your `.mzML` files (MS/MS data), `.fasta` files (protein database), and `.xlsx` file (oxonium ion definitions) in the `Input` directory + - The DirectTag executable files are already included in the `directag_windows_64bits` directory for Windows and `directag_linux_64bit` directory for Linux + +3. Build the Docker image: + ```bash + docker build -t novoglyco . + ``` + +4. **Run NovoGlyco** using one of the following methods: + + First, ensure any previous NovoGlyco container is removed: + ```bash + docker rm -f novoglyco + ``` + + ### Option 1: Single Command (recommended for first-time runs) + + Run both DirectTag and Docker together with a single command: + + **For Windows (Command Prompt):** + ``` + start "DirectTag Process" cmd /c run_directag_windows.bat &amp; docker run --name novoglyco -p 8050:8050 -v "%cd%\Input:/app/Input" -v "%cd%\Output:/app/Output" novoglyco + ``` + + **For Windows (PowerShell):** + ``` + Start-Process -FilePath "cmd" -ArgumentList "/c run_directag_windows.bat"; docker run --name novoglyco -p 8050:8050 -v "${PWD}\Input:/app/Input" -v "${PWD}\Output:/app/Output" novoglyco + ``` + + **For Linux/macOS:** + ``` + ./run_directag_linux.sh &amp; docker run --name novoglyco -p 8050:8050 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" novoglyco + ``` + + ### Option 2: Separate Commands + + Run both processes in separate terminal windows: + + **Terminal 1 - Start DirectTag script:** + + For Windows: + ``` + run_directag_windows.bat + ``` + + For Linux: + ``` + ./run_directag_linux.sh + ``` + + **Terminal 2 - Start Docker container:** + + For Windows Command Prompt: + ``` + docker run --name novoglyco -p 8050:8050 -v "%cd%\Input:/app/Input" -v "%cd%\Output:/app/Output" novoglyco + ``` + + For PowerShell: + ``` + docker run --name novoglyco -p 8050:8050 -v "${PWD}\Input:/app/Input" -v "${PWD}\Output:/app/Output" novoglyco + ``` + + For Linux/macOS: + ``` + docker run --name novoglyco -p 8050:8050 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" novoglyco + ``` + + ### Option 3: Docker Only (when tags are already generated) + + If you already have DirectTag tags files in your Input directory with the desired tag length, you can skip the DirectTag execution and run only the Docker container: + + For Windows Command Prompt: + ``` + docker run --name novoglyco -p 8050:8050 -v "%cd%\Input:/app/Input" -v "%cd%\Output:/app/Output" novoglyco + ``` + + For PowerShell: + ``` + docker run --name novoglyco -p 8050:8050 -v "${PWD}\Input:/app/Input" -v "${PWD}\Output:/app/Output" novoglyco + ``` + + For Linux/macOS: + ``` + docker run --name novoglyco -p 8050:8050 -v "$(pwd)/Input:/app/Input" -v "$(pwd)/Output:/app/Output" novoglyco + ``` + + **Note:** For the Docker-only approach to work, there must be a tags file in the Input directory named exactly `[mzML_filename]_DIRECTAG_top10_tag[Tag_Length].tags`. If you've previously generated tags with a different naming convention, make sure to rename them accordingly. + + +5. Access the interactive dashboard + - Open your browser and navigate to: `http://localhost:8050` + +6. Results will be saved to the `Output` directory + +7. To analyze the next set of data or use different parameters: + - Press `Ctrl+C` to stop the current container (Note: This may not fully exit the container) + - Run `docker ps` to identify any containers still running: + ``` + docker ps + ``` + - Stop any running NovoGlyco containers: + ``` + docker stop [CONTAINER_ID] + ``` + or to stop all running containers: + ``` + docker stop $(docker ps -q) + ``` + - Replace the input files in the `Input` directory + - Run the Docker command again with desired parameters (see "Running with Custom Parameters" section) + NOTE: Output will be overwritten if the same input files are used + + +## License + +NovoGlyco is released under the Apache License 2.0. + +Copyright (c) 2025 + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this software except in compliance with the License. +You may obtain a copy of the License at: + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + +Please note that some of the functions and libraries used by NovoGlyco may not share the same license as NovoGlyco. +If you want to use any of these in a different context, ensure that you obtain the appropriate licenses for the dependent libraries and tools. +Additional info dependencies and functions (not complete): + +Python: Python 3.x, open-source, https://www.python.org/ +Dash: MIT License, https://dash.plotly.com/ +Pyteomics: MIT License, https://pyteomics.readthedocs.io/ +pandas: BSD 3-Clause License, https://pandas.pydata.org/ +matplotlib: Matplotlib is licensed under the PSF License, https://matplotlib.org/ +scipy: BSD 3-Clause License, https://scipy.org/ +numpy: BSD 3-Clause License, https://numpy.org/ +Sage: MIT License, https://github.com/lazear/sage (Used for advanced spectrum annotation and pre-filtering) +Lazear, Michael R. "Sage: an open-source tool for fast proteomics searching and quantification at scale." +Journal of Proteome Research 22.11 (2023): 3652-3659. +Other Python Libraries: Please review the licenses for any other third-party packages used. +Version/History: Version 1.0.0 + +Future versions will continue to improve functionality and performance, with regular updates to fix bugs and add features. + +Data/Privacy: +NovoGlyco does not collect, store, or transmit any personal data. It operates entirely on the local machine and does not interact with any external servers or services. All data processing and analysis occur locally, and the application does not send or receive any data over the internet unless specifically configured to do so (e.g., if the user chooses to share files for support purposes). +Data Collection: No data is collected by the Oxonium Explorer itself. However, any files processed using Oxonium Explorer (such as proteomics data files) are handled on the user's local machine and are not transmitted unless manually shared by the user. +Data Security: Oxonium Explorer does not store any sensitive data and does not have access to personal or confidential information. All data handling is kept within the scope of the users local environment, and files are not uploaded or shared without explicit user action. +Privacy Policy: Since Oxonium Explorer does not engage in data collection or sharing, a privacy policy is not required. However, users should ensure they are aware of the privacy policies of any external tools or libraries that may collect data in their respective functionalities. +User Consent: By using Oxonium Explorer, you consent to the software operating on your local machine as described above, and you are responsible for managing your own data and files. + +No Warranty Disclaimer: +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES, OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +Please ensure you are complying with the terms and conditions of the dependencies and their respective licenses. + +## Citation + +If you use this software in your research, please cite: +Soic D and Pabst M. NovoGlyco: mapping protein glycosylation in prokaryotes. bioRxiv. 2025. + +## Contacts + +Dinko Soic (dsoic@pharma.hr) +Martin Pabst (m.pabst@tudelft.nl) </pre> </div>Dinko SoicThu, 29 May 2025 13:59:53 -0000https://sourceforge.net6c3b8640d8ef0c828df98ea758d840e7a6fa88a3https://sourceforge.net/p/novoglycox/wiki/Home/<div class="markdown_content"><p>Welcome to your wiki!</p> <p>This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: <span>[SamplePage]</span>.</p> <p>The wiki uses <a class="" href="/p/novoglycox/wiki/markdown_syntax/" rel="nofollow">Markdown</a> syntax.</p> <p></p><h6>Project Members:</h6> <ul class="md-users-list"> <li><a href="/u/glycolab/">glycolab</a> (admin)</li> </ul><br/> <p><span class="download-button-68386700514a2f3bb245e9eb" style="margin-bottom: 1em; display: block;"></span></p><p></p></div>glycolabThu, 29 May 2025 13:54:09 -0000https://sourceforge.netd4835d1dbedf7a59c7c45d11474f9c6239670b21