arXiv subjects

Bilal Shaikh

Publications and source records attributed to Bilal Shaikh.

4 recordsLinked to original sources

arXiv2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML, and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

q-bio.QM↗

arXiv2021

SED-ML Validator: tool for debugging simulation experiments

Summary: More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such models, the community developed the Simulation Experiment Description Markup Language (SED-ML), a common format for describing simulations. However, the utility of SED-ML has been hampered by limited support for SED-ML among modeling software tools and by different interpretations of SED-ML among the tools that support the format. To help modelers debug their simulations and to push the community to use SED-ML consistently, we developed a tool for validating SED-ML files. We have used the validator to correct the official SED-ML example files. We plan to use the validator to correct the files in the BioModels database so that they can be simulated. We anticipate that the validator will be a valuable tool for developing more predictive simulations and that the validator will help increase the adoption and interoperability of SED-ML. Availability: The validator is freely available as a webform, HTTP API, command-line program, and Python package at https://run.biosimulations.org/utils/validate and https://pypi.org/project/biosimulators-utils. The validator is also embedded into interfaces to 11 simulation tools. The source code is openly available as described in the Supplementary data. Contact: karr@mssm.edu

q-bio.QM↗

arXiv2020

ObjTables: structured spreadsheets that promote data quality, reuse, and integration

A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous information. Supplementary spreadsheets to articles are a key data source. Spreadsheets are popular because they are easy to read and write. However, spreadsheets are often difficult to reanalyze because they capture data ad hoc without schemas that define the objects, relationships, and attributes that they represent. To help researchers reuse and compose spreadsheets, we developed ObjTables, a toolkit that makes spreadsheets human- and machine-readable by combining spreadsheets with schemas and an object-relational mapping system. ObjTables includes a format for schemas; markup for indicating the class and attribute represented by each spreadsheet and column; numerous data types for scientific information; and high-level software for using schemas to read, write, validate, compare, merge, revision, and analyze spreadsheets. By making spreadsheets easier to reuse, ObjTables could enable unprecedented secondary meta-analyses. By making it easy to build new formats and associated software for new types of data, ObjTables can also accelerate emerging scientific fields.

cs.DB↗

arXiv2019

BpForms and BcForms: Tools for concretely describing non-canonical polymers and complexes to facilitate comprehensive biochemical networks

Although non-canonical residues, caps, crosslinks, and nicks play an important role in the function of many DNA, RNA, proteins, and complexes, we do not fully understand how networks of non-canonical macromolecules generate behavior. One barrier is our limited formats, such as IUPAC, for abstractly describing macromolecules. To overcome this barrier, we developed BpForms and BcForms, a toolkit of ontologies, grammars, and software for abstracting the primary structure of polymers and complexes as combinations of residues, caps, crosslinks, and nicks. The toolkit can help quality control, exchange, and integrate information about the primary structure of macromolecules into fine-grained global networks of intracellular biochemistry.

q-bio.BM↗