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Mol*: Towards a Common Library and Tools for Web Molecular Graphics Workshop on Molecular Graphics and Visual Analysis of Molecular Data (2018) J. Byška, M. Krone, and B. Sommer (Editors) Mol*: Towards a common library and tools for web molecular graphics D. Sehnal1;2;4, A. S. Rose3, J. Kocaˇ 1;2, S. K. Burley3;5 and S. Velankar4 1CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic 2National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic 3RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA 4Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK 5RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA Abstract Advances in experimental techniques are providing access to structures of ever more complex and larger macromolecular systems. Web-browser based visualization and analysis of macromolecular structures and associated data represents a crucial step in gaining knowledge from these data. A common library and a set of tools for working with such macromolecular data sets would streamline this step. We present a project called Mol* (/’mol-star/) whose goal is to provide a common library and a set of tools for macromolecular data visualization and analysis. The project includes modules for data storage, in-memory representation, query language, UI state management, and visualization; and tools for efficient data access. CCS Concepts •Computing methodologies ! Rendering; Graphics systems and interfaces; •Applied computing ! Bioinformatics; 1. Introduction (most notably JavaScript, HTML, and WebGL) and their surround- Experimental methods to determine three-dimensional (3D) struc- ing ecosystem (including NPM, Node.js, TypeScript, GitHub) offer tures of biomolecules are being continuously improved and pro- good support for the development of modular libraries/components. duce molecular complexes from models of different resolutions Taken together, the web provides a unique opportunity to develop that span multiple scales and can be dynamic over the course a common library and a set of tools for accessing, analyzing, and of an experiment. By combining data from complementary ex- visualizing macromolecular data. perimental techniques (e.g., X-ray, NMR, 3DEM, SAS, chemi- Here we introduce Mol* (/’mol-star/), an open source project cal crosslinking) or integrative/hybrid methods (I/HM), 3D struc- supported/maintained by RCSB Protein Data Bank (PDB) [Ber00] tural models of large macromolecular systems can be determined and Protein Data Bank in Europe (PDBe) [MAA∗18] with the goal [BKM∗17, SBS∗15]. Such models include large macromolecular of developing a common library and tools for web-based molecular machines, dynamic assemblies, or genome architecture. Access, vi- graphics and analyses. The project includes modules for data stor- sualization and analysis of these structures is a central part of struc- age, in-memory representation, a query language, UI state manage- tural biology and structural bioinformatics. However, as macro- ment, visualization, and tools for efficient data access. In develop- molecular data sets grow ever more complex and larger, it becomes ing Mol* as a collection of interoperable modules, we are creating challenging to create software tools to access, visualize and manip- an ecosystem that will support community contributions at all lev- ulate them. The web platform, both mobile and desktop, is becom- els of the framework. Building on a common library can help con- ing an increasingly popular and important tool for performing these tributors focus on innovative visualization and algorithms. It can tasks. offer visualization researchers and algorithm developers a means Embracing recent advances in web browser technology provides to make their research more widely available and used in practice. the means for creating scalable molecular graphics and analysis Furthermore, collaborative development can also help with antici- tools with near-instant access to any available data. Web-based pating and keeping up with developments in structural biology and tools are platform-independent and require little or no local soft- related fields by pooling/sharing resources. ware installation, which makes them available to virtually every- The purpose of Mol* is to enable web-based molecular visual- one in both the scientific and non-scientific community, reaching ization and analyses by providing a common library for quickly an audience larger than ever before. Moreover, these technologies and efficiently building tools and services for the structural biol- c 2018 The Author(s) Eurographics Proceedings c 2018 The Eurographics Association. DOI: 10.2312/molva.20181103 30 D. Sehnal & A. S. Rose / Mol*: Towards a common library and tools for web molecular graphics ogy/bioinformatics community. Examples include showing experi- PyMol, VMD, or Jmol into MolQL to enable backwards com- mental/validation related data for macromolecular models; display- patibility. The language runtime can be implemented in various ing various annotations for macromolecular models providing bio- programming languages, as MolQL only defines what queries logical context, including SCOP, PFAM, UniProt; the creation of should be available and what the results should look like. More visually interesting, engaging and interactive educational material; information about MolQL, its initial specification and reference or visualizing results from structural bioinformatics or computer implementation are available at github.com/MolQL. aided drug design algorithms. Common state description The state description of the viewer is The project builds on the code and knowledge the authors gained abstracted into a DSL as well. The advantage of this approach from developing web-based molecular viewers, analysis tools and is that the state description could be more easily parsed by other compressed file formats, including the LiteMol Suite [SDV∗17], software (including desktop applications). This language could the NGL Viewer [RH15, RBV∗16], PatternQuery [SPS∗15], and also have the potential to evolve into a standard for describing MMTF [BRP∗17, VBR∗17]. Mol* is developed as an open source visualizations in publications. As with MolQL, we hope that the project and hosted on GitHub (github.com/mol-star). language will be implemented in other programming languages. We want to investigate the possibility of interpreting PyMOL, 2. Mol* Overview Jmol, VMD, etc. scripts to describe application state. Successful web applications require the right tradeoff between net- Data access tools Modern experimental and computation methods work bandwidth/latency and client-side computations. This need is produce large amounts of data and it is often not feasible to trans- especially relevant to molecular visualizations and analyses as be- fer all this data at the same time due to bandwidth/memory con- ing data heavy and/or computation heavy. Mwalongo et al. describe straints. To overcome these limitations we want to implement four criteria to classify web-based visualization tools [MKRE16]. possible solutions, including sending subsets of the data, down- These are: sampled data, introducing new/better compression methods. • Infrastructure (web service, grid-based, cloud-based, local). Ability to share code between client and server Some analyses • Data transfer (full, progressive, simplified). can be run directly in the web browser and utilize the compu- • Rendering techniques (volume, raycasting, triangle mesh). tational power of the user’s computer. More demanding compu- • Optimization targets (latency, bandwidth, rendering). tations can be executed on the server. The goal of Mol* is to provide a framework that spans the server and the client so that computations can be performed using the Modularity Different libraries/modules/tools of Mol* should be same library on the server and the client depending on the opti- usable separately. This ensures that Mol* could be partially inte- mization target. grated into existing projects. High performance A high emphasis will be put on the perfor- 2.1. Core Concepts mance of individual modules. The core philosophy of Mol* is to provide means for high degree of interoperability with existing and future solutions. This is mainly achieved by: 1) supporting existing file formats (and extending on 2.2. Project Structure them where appropriate or required, e.g., mmCIF and BinaryCIF), The project structure is separated into three main parts: 1) core and, 2) instead of creating a scripting language that would operate modules, 2) data access tools, and 3) application modules; all are only within the Mol* ecosystem (similar to PyMOL or Jmol ap- described below. proach), defining a set of open domain specific languages (DSL) which Mol* only provides a reference implementation for. The ba- sic concepts that expand on this idea are outlined below. 2.2.1. Core Modules Common data/exchange formats A small set of data for- The core modules of Mol* provide basic data structures and algo- mats/layouts is used for all data exchange within Mol*. The rithms that more complex applications can build upon. BinaryCIF data format is utilized heavily. BinaryCIF is a bi- nary encoding of the text based mmCIF that maintains the ver- Mol-data A set of common
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