Nathan Edwards

18 papers B 1C 2Journal 8Unranked 7
YearRankTypeTitle / Venue / Authors
2023 J jnl
CoRR
Aida Damanpak Rizi, Antika Roy, Rouhan Noor, Hyo Kang, Nitin Varshney, Katja Jacob, Sindia Rivera-Jimenez, Nathan Edwards, Volker J. Sorger, Hamed Dalir, Navid Asadizanjani
2023 J jnl
Bioinform.
Nathan Edwards, Christian Dillard, N. M. Prashant, Liu Hongyu, Mia Yang, Evgenia Ulianova, Anelia Horvath
2020 J jnl
Bioinform.
Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder
2020 conf
SP (Workshops)
Brett Meadows, Nathan Edwards, Sang-Yoon Chang
2017 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu
2014 conf
BCB
Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu
2011 J jnl
IEEE Trans. Instrum. Meas.
Jacob Rosenthal, Nathan Edwards, Daniel Villanueva, Sreekar Krishna, Troy McDaniel, Sethuraman Panchanathan
2010 J jnl
Int. J. Comput. Integr. Manuf.
Ning Fang, P. Srinivasa Pai, Nathan Edwards
2007 J jnl
J. Comput. Biol.
Xue Wu, Chau-Wen Tseng, Nathan Edwards
2006 conf
Systems Biology and Computational Proteomics
Daniel P. Fasulo, Anne-Katrin Emde, Lu-Yong Wang, Karin Noy, Nathan Edwards
2006 J jnl
Adv. Comput.
Xue Wu, Nathan Edwards, Chau-Wen Tseng
2004 C conf
WABI
Nathan Edwards, Ross Lippert
2003 conf
DMTCS
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
2003 B conf
RECOMB
Vineet Bafna, Nathan Edwards
2002 conf
Computational Methods for SNPs and Haplotype Inference
Bjarni V. Halldórsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail
2002 C conf
WABI
Nathan Edwards, Ross Lippert
2001 conf
ISMB (Supplement of Bioinformatics)
Vineet Bafna, Nathan Edwards
2001 conf
IEEE Symposium on Parallel and Large-Data Visualization and Graphics
Russell J. Turner, Kabir Chaturvedi, Nathan Edwards, Daniel P. Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail
docs/linting.md
← Index docs/linting.md markdown
# Code Linting Guide

## Installation

```bash
pip install flake8 pylint black isort
```

## Quick Usage

### Check Code Quality
```bash
# Comprehensive analysis (recommended)
pylint redb/

# Quick style check
flake8 redb/

# Format code
black redb/

# Sort imports
isort redb/
```

### Check Only (No Changes)
```bash
black --check redb/
isort --check-only redb/
```

## Configuration

The project uses `pyproject.toml` for configuration. Key settings:

- **Line length**: 120 characters
- **Pylint**: Disabled overly strict warnings (docstrings, naming conventions)
- **Black**: Compatible with isort
- **Flake8**: Ignores common style issues

## Security-Focused Linting

For security analysis, install additional tools:

```bash
pip install pylint-security bandit
```

Run security checks:
```bash
# Pylint with security plugin
pylint --load-plugins=pylint_security redb/

# Bandit (security-focused)
bandit -r redb/
```

## Recommended Workflow

1. **Development**: Use `flake8` for quick feedback
2. **Pre-commit**: Run `pylint` for comprehensive analysis
3. **Formatting**: Use `black` and `isort` before commits
4. **Security**: Run `bandit` periodically

## IDE Integration

Most IDEs support these tools:
- **VS Code**: Install Python extension, configure linting
- **PyCharm**: Built-in support for all tools
- **Vim/Neovim**: Use ALE or similar plugins