The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the and genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the and genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community.

RNAget: an API to securely retrieve RNA quantifications.

Summary: Large-scale sharing of genomic quantification data requires standardized access interfaces. In this Global Alliance for Genomics and Health project, we developed RNAget, an API for secure access to genomic quantification data in matrix form. RNAget provides for slicing matrices to extract desired subsets of data and is applicable to all expression matrix-format data, including RNA sequencing and microarrays.

An artificial intelligence enabled chemical synthesis robot for exploration and optimization of nanomaterials.

We present an autonomous chemical synthesis robot for the exploration, discovery, and optimization of nanostructures driven by real-time spectroscopic feedback, theory, and machine learning algorithms that control the reaction conditions and allow the selective templating of reactions. This approach allows the transfer of materials as seeds between cycles of exploration, opening the search space like gene transfer in biology. The open-ended exploration of the seed-mediated multistep synthesis of gold nanoparticles (AuNPs) via in-line ultraviolet-visible characterization led to the discovery of five categories of nanoparticles by only performing ca.

Digitization and validation of a chemical synthesis literature database in the ChemPU.

Despite huge potential, automation of synthetic chemistry has only made incremental progress over the past few decades. We present an automatically executable chemical reaction database of 100 molecules representative of the range of reactions found in contemporary organic synthesis. These reactions include transition metal-catalyzed coupling reactions, heterocycle formations, functional group interconversions, and multicomponent reactions.

A robotic prebiotic chemist probes long term reactions of complexifying mixtures.

To experimentally test hypotheses about the emergence of living systems from abiotic chemistry, researchers need to be able to run intelligent, automated, and long-term experiments to explore chemical space. Here we report a robotic prebiotic chemist equipped with an automatic sensor system designed for long-term chemical experiments exploring unconstrained multicomponent reactions, which can run autonomously over long periods. The system collects mass spectrometry data from over 10 experiments, with 60 to 150 algorithmically controlled cycles per experiment, running continuously for over 4 weeks.

Identifying molecules as biosignatures with assembly theory and mass spectrometry.

The search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry.

A universal system for digitization and automatic execution of the chemical synthesis literature.

Robotic systems for chemical synthesis are growing in popularity but can be difficult to run and maintain because of the lack of a standard operating system or capacity for direct access to the literature through natural language processing. Here we show an extendable chemical execution architecture that can be populated by automatically reading the literature, leading to a universal autonomous workflow. The robotic synthesis code can be corrected in natural language without any programming knowledge and, because of the standard, is hardware independent.

A Modular Programmable Inorganic Cluster Discovery Robot for the Discovery and Synthesis of Polyoxometalates.

The exploration of complex multicomponent chemical reactions leading to new clusters, where discovery requires both molecular self-assembly and crystallization, is a major challenge. This is because the systematic approach required for an experimental search is limited when the number of parameters in a chemical space becomes too large, restricting both exploration and reproducibility. Herein, we present a synthetic strategy to systematically search a very large set of potential reactions, using an inexpensive, high-throughput platform that is modular in terms of both hardware and software and is capable of running multiple reactions with in-line analysis, for the automation of inorganic and materials chemistry.

A nanomaterials discovery robot for the Darwinian evolution of shape programmable gold nanoparticles.

The fabrication of nanomaterials from the top-down gives precise structures but it is costly, whereas bottom-up assembly methods are found by trial and error. Nature evolves materials discovery by refining and transmitting the blueprints using DNA mutations autonomously. Genetically inspired optimisation has been used in a range of applications, from catalysis to light emitting materials, but these are not autonomous, and do not use physical mutations.

The ENCODE Portal as an Epigenomics Resource.

The Encyclopedia of DNA Elements (ENCODE) web portal hosts genomic data generated by the ENCODE Consortium, Genomics of Gene Regulation, The NIH Roadmap Epigenomics Consortium, and the modENCODE and modERN projects. The goal of the ENCODE project is to build a comprehensive map of the functional elements of the human and mouse genomes. Currently, the portal database stores over 500 TB of raw and processed data from over 15,000 experiments spanning assays that measure gene expression, DNA accessibility, DNA and RNA binding, DNA methylation, and 3D chromatin structure across numerous cell lines, tissue types, and differentiation states with selected genetic and molecular perturbations.

Organic synthesis in a modular robotic system driven by a chemical programming language.

The synthesis of complex organic compounds is largely a manual process that is often incompletely documented. To address these shortcomings, we developed an abstraction that maps commonly reported methodological instructions into discrete steps amenable to automation. These unit operations were implemented in a modular robotic platform by using a chemical programming language that formalizes and controls the assembly of the molecules.

Networking chemical robots for reaction multitasking.

The development of the internet of things has led to an explosion in the number of networked devices capable of control and computing. However, whilst common place in remote sensing, these approaches have not impacted chemistry due to difficulty in developing systems flexible enough for experimental data collection. Herein we present a simple and affordable (<$500) chemistry capable robot built with a standard set of hardware and software protocols that can be networked to coordinate many chemical experiments in real time.

Prevention of data duplication for high throughput sequencing repositories.

https://www.encodeproject.org/.

The Encyclopedia of DNA elements (ENCODE): data portal update.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface.