bioLQM: a java library for the manipulation and conversion of Logical Qualitative Models of biological networks

Naldi, Aurélien

doi:10.1101/287011

Cited by 4 publications

(5 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For dependency management of external libraries, EpiLog relies on Apache Maven. A particular library is the bioLQM Java toolkit (Logical Qualitative Models of biological regulatory networks), for the representation and manipulation of logical, cellular models, available at https://github.com/colomoto/bioLQM 10 .…”

Section: Methodsmentioning

confidence: 99%

EpiLog: A software for the logical modelling of epithelial dynamics

Varela¹,

Ramos

Monteiro

et al. 2018

F1000Res

View full text Add to dashboard Cite

Cellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical (Boolean or multi-valued) framework proved well suited to study such processes at the cellular level, by specifying qualitative models of involved signalling pathways and gene regulatory networks. Here, we describe and illustrate the main features of EpiLog, a computational tool that implements an extension of the logical framework to the tissue level. EpiLog defines a collection of hexagonal cells over a 2D grid, which embodies a mono-layer epithelium. Basically, it defines a cellular automaton in which cell behaviours are driven by associated logical models subject to external signals. EpiLog is freely available on the web at http://epilog-tool.org. It is implemented in Java (version ≥1.7 required) and the source code is provided at https://github.com/epilog-tool/epilog under a GNU General Public License v3.0.

show abstract

Section: Methodsmentioning

confidence: 99%

EpiLog: A software for the logical modelling of epithelial dynamics

Varela¹,

Ramos

Monteiro

et al. 2018

F1000Res

View full text Add to dashboard Cite

show abstract

“…The presence of multiple (disjoint) attractors can represent alternative cell fates (such as cell differentiation states), while cyclic attractors further represent periodic behaviours (such as cell cycle or circadian rhythms). The computation of attractors is addressed by different software tools, such as bioLQM [31], GINsim [32], Pint [36], BoolSim [19], BooleanNet [3], pyBoolNet [25], and…”

Section: Dynamical Analysismentioning

confidence: 99%

“…bioLQM-Qualitative model toolbox The biolqm Python module provides direct access to the Java programming interface of bioLQM [31]. bioLQM is available and documented at http://colomoto.…”

Section: Model Input and Tool Conversionsmentioning

confidence: 99%

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Naldi

Hernandez

Levy

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Analysing models of biological networks typically relies on workflows in which different software tools with sensitive parameters are chained together, many times with additional manual steps.The accessibility and reproducibility of such workflows is challenging, as publications often overlook analysis details, and because some of these tools may be difficult to install, and/or have a steep learning curve. The CoLoMoTo Interactive Notebook provides a unified environment to edit, execute, share, and reproduce analyses of qualitative models of biological networks. This framework combines the power of different technologies to ensure repeatability and to reduce users' learning curve of these technologies. The framework is distributed as a Docker image with the tools ready to be run without any installation step besides Docker, and is available on Linux, macOS, and Microsoft Windows. The embedded computational workflows are edited with a Jupyter web interface, enabling the inclusion of textual annotations, along with the explicit code to execute, as well as the visualisation of the results.The resulting notebook files can then be shared and re-executed in the same environment. To date, the CoLoMoTo Interactive Notebook provides access to software tools including GINsim, BioLQM, Pint, MaBoSS, and Cell Collective for the modelling and analysis of Boolean and multi-valued networks.More tools will be included in the future. We developed a Python interface for each of these tools to offer a seamless integration in the Jupyter web interface and ease the chaining of complementary analyses. Python programming languageRecently, the scientific community has been increasingly concerned about difficulties in reproducing already published results. In the context of preclinical studies, observed difficulties to reproduce important findings have raised controversy (see e.g. [7,15,40,43], and [8] for a review on this topic). Although not invalidating the findings, these observations have shaken the community. In 2016, a Nature survey pointed to the multi-factorial origin of this "reproducibility crisis" [4]. Factors related to computational analyses were highlighted, in particular the unavailability of code and methods, along with the technical expertise required to reproduce the computations.The scientific community is progressively addressing this problem. Prestigious conferences (such as two major conferences from the database community, namely, VLDB 1 and SIGMOD 2 ) and journals such as PNAS 3 , Biostatistics [38], Nature [41] and Science [54], to name only a few, now encourage or even require published results to be accompanied by all the information necessary to reproduce them. While the reproducibility challenges have first been observed in domains where deluge of data were quickly becoming available (e.g., Next Generation Sequencing data analyses), the problem is now present in many (if not all) communities where computational analyses and simulations are performed. In particular, the System Biology community is facing a pro...

show abstract

“…First, we compute the complete list of logical stable states (or fixpoints) of the model using the Java library (Naldi, 2018 ). We thus need to convert the GINsim model into bioLQM:…”

Section: Stepwise Proceduresmentioning

confidence: 99%

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

et al. 2018

Self Cite

View full text Add to dashboard Cite

Boolean and multi-valued logical formalisms are increasingly used to model complex cellular networks. To ease the development and analysis of logical models, a series of software tools have been proposed, often with specific assets. However, combining these tools typically implies a series of cumbersome software installation and model conversion steps. In this respect, the CoLoMoTo Interactive Notebook provides a joint distribution of several logical modeling software tools, along with an interactive web Python interface easing the chaining of complementary analyses. Our computational workflow combines (1) the importation of a GINsim model and its display, (2) its format conversion using the Java library BioLQM, (3) the formal prediction of mutations using the OCaml software Pint, (4) the model checking using the C++ software NuSMV, (5) quantitative stochastic simulations using the C++ software MaBoSS, and (6) the visualization of results using the Python library matplotlib. To illustrate our approach, we use a recent Boolean model of the signaling network controlling tumor cell invasion and migration. Our model analysis culminates with the prediction of sets of mutations presumably involved in a metastatic phenotype.

show abstract

bioLQM: a java library for the manipulation and conversion of Logical Qualitative Models of biological networks

Cited by 4 publications

References 40 publications

EpiLog: A software for the logical modelling of epithelial dynamics

EpiLog: A software for the logical modelling of epithelial dynamics

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)

Contact Info

Product

Resources

About