Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: SMBL

https://packages.ecosyste.ms/registries/pypi.org/packages/SMBL

SnakeMake Bioinformatics Library.
24 versions
Latest release: about 1 year ago
16 downloads last month

Papers Mentioning SMBL 20

Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map
Cited by: 10
Author(s): Quentin Miagoux, Vidisha Singh, Dereck de Mézquita, Valérie Chaudru, Mohamed Elati, Élisabeth Petit-Teixeira, Anna Niarakis
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0252759

Antimicrobial activity of methanolic extracts of Vernonia cinerea against Xanthomonas oryzae and identification of their compounds using in silico techniques
Cited by: 6
Author(s): Tushar Joshi, Satish Chandra Pandey, Priyanka Maiti, Manish Kumar Tripathi, Ashutosh Paliwal, Mahesha Nand, Priyanka Sharma, Mukesh Samant, Veena Pande, Subhash Chandra
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-10-S12-S7

XML-based approaches for the integration of heterogeneous bio-molecular data
Cited by: 26
Author(s): Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga, Paolo Perlasca, Giorgio Valentini, David Manset
Software Mentions: 4
Published: about 15 years ago

10.1371/journal.pone.0038518

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion
Cited by: 47
Author(s): Philipp Thomas, Hannes Matuschek, Ramon Grima
Software Mentions: 3
Published: over 12 years ago

10.1093/bib/bby025

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures
Cited by: 16
Author(s): Mansoor Saqi, Artem Lysenko, Yike Guo, Tatsuhiko Tsunoda, Charles Auffray
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2021.710590

A Life Cycle for Modeling Biology at Different Scales
Cited by: 3
Author(s): Kate Harline, Jesús Martínez‐Gómez, Chelsea D. Specht, Adrienne Roeder
Software Mentions: 2
Published: about 3 years ago

10.1186/1756-0381-1-12

A survey of visualization tools for biological network analysis
Cited by: 197
Author(s): Georgios A. Pavlopoulos, Anna-Lynn Wegener, Reinhard Schneider
Software Mentions: 2
Published: almost 16 years ago

10.1186/1752-0509-2-104

Arena3D: visualization of biological networks in 3D
Cited by: 98
Author(s): Georgios A. Pavlopoulos, Seán I. O’Donoghue, Venkata Satagopam, Theodoros Soldatos, Evangelos Pafilis, Reinhard Schneider
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0023026

Predicting the Physiological Role of Circadian Metabolic Regulation in the Green Alga Chlamydomonas reinhardtii
Cited by: 7
Author(s): Sascha Schäuble, Ines Heiland, Olga Voytsekh, Maria Mittag, Stefan Schuster
Software Mentions: 2
Published: over 13 years ago

10.1186/1752-0509-5-204

Heterogeneity reduces sensitivity of cell death for TNF-Stimuli
Cited by: 38
Author(s): Monica Schliemann, Eric Bullinger, Steffen Borchers, Frank Allgöwer, Rolf Findeisen, Peter Scheurich
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0182385

Modeling and simulation of biological systems using SPICE language
Cited by: 11
Author(s): Morgan Madec, Christophe Lallement, Jacques Haiech
Software Mentions: 2
Published: over 7 years ago

10.3389/fpls.2014.00724

Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
Cited by: 31
Author(s): Jordan O. Hay, Hai Ning Shi, Nicolas Heinzel, Inga Hebbelmann, Hardy Rolletschek, Jörg Schwender
Software Mentions: 2
Published: almost 10 years ago

10.1186/1479-5876-12-S2-S7

Simulation environment and graphical visualization environment: a COPD use-case
Cited by: 7
Author(s): Mercedes Huertas-Migueláñez, Daniel Mora-Meliá, Isaac Cano, Dieter Maier, David Gomez-Cabrero, Magí Lluch-Ariet, Felip Miralles
Software Mentions: 1
Published: almost 11 years ago

10.1186/1752-0509-6-52

AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease
Cited by: 113
Author(s): Satoshi Mizuno, Risa Iijima, Soichi Ogishima, Masataka Kikuchi, Yoshikazu Matsuoka, Samik Ghosh, Tadashi Miyamoto, Akinori Miyashita, Ryozo Kuwano, Hiroshi Tanaka
Software Mentions: 1
Published: over 12 years ago

10.1186/1752-0509-4-40

Stochastic Modeling of B Lymphocyte Terminal Differentiation and Its Suppression by Dioxin
Cited by: 24
Author(s): Qiang Zhang, Sudin Bhattacharya, Douglas E. Kline, R. J. Crawford, Rory B. Conolly, Russell S. Thomas, Norbert E. Kaminski, Melvin E. Andersen
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0055190

Systems Modelling of NHEJ Reveals the Importance of Redox Regulation of Ku70/80 in the Dynamics of DNA Damage Foci
Cited by: 18
Author(s): David Dolan, Glyn Nelson, Anže Županič, Graham R. Smith, Daryl P. Shanley
Software Mentions: 1
Published: almost 12 years ago

10.1093/database/baw113

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)
Cited by: 24
Author(s): Juliane Fluck, Sumit Madan, Sam Ansari, Alpha Tom Kodamullil, Reagon Karki, Majid Rastegar-Mojarad, Natalie L. Catlett, William Hayes, Justyna Szostak, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 1
Published: almost 9 years ago

10.3389/fbioe.2020.00942

Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology
Cited by: 22
Author(s): Lucia Marucci, Matteo Barberis, Jonathan R. Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan A. Hoffmann, Sophie Landon, E. L. Rech, Joshua Rees-Garbutt, Richard Seabrook, W. M. Shaw, Christopher Woods
Software Mentions: 1
Published: over 4 years ago

10.1186/s12859-019-3101-1

Quantifying mechanisms in neurodegenerative diseases (NDDs) using candidate mechanism perturbation amplitude (CMPA) algorithm
Cited by: 3
Author(s): Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt, Martin Hofmann-Apitius
Software Mentions: 1
Published: about 5 years ago