A3D 2.0 update for the prediction and optimization of protein solubility

Protein aggregation propensity is a property imprinted in protein sequences and structures, being associated with the onset of human diseases and limiting the implementation of protein-based biotherapies. Computational approaches stand as cost-effective alternatives for reducing protein aggregation and increasing protein solubility. AGGRESCAN 3D (A3D) is a structure-based predictor of aggregation that takes into account the conformational context of a protein, aiming to identify aggregation-prone regions exposed in protein surfaces. Here we inspect the updated 2.0 version of the algorithm, which extends the application of A3D to previously inaccessible proteins and incorporates new modules to assist protein redesign. Among these features, the new server includes stability calculations and the possibility to optimize protein solubility using an experimentally validated computational pipeline. Finally, we employ defined examples to navigate the A3D RESTful service, a routine to handle extensive protein collections. Altogether, this work is conceived to train and assist A3D non-experts in the study of aggregation-prone regions and protein solubility redesign.

Curation of over 10 000 transcriptomic studies to enable data reuse

Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe–gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma’s holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. Database URL: https://gemma.msl.ubc.ca/home.html

Curation of over 10,000 transcriptomic studies to enable data reuse

Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing is necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface, and web services. Here we present an update on Gemma’s holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10,811 manually curated datasets (primarily human, mouse, and rat), over 395,000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA-sequencing). Dataset topics were represented with 10,215 distinct terms from 12 ontologies, for a total of 54,316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service, and an R package.Database URL: https://gemma.msl.ubc.ca/home.html

A General Overview of RESTful Web Services

This chapter aims to present a general overview of today's dominant software architectural style for developing web services, namely REST, by comparing the core elements of this paradigm with the big web service model. The study evaluates the HTTP requests, responses, and thus, the SOAP/JSON payloads involved in consuming a big web service and a RESTful service that is developed in the ASP.NET Core Web API framework. After summarizing the REST constraints, the chapter elucidates how the example RESTful web service satisfies these constraints and lists some scenarios suited to each paradigm. The study notes the object-oriented elements that are inherent in RESTful services, specifically how polymorphism and abstraction principles can be applied to RESTful services.

Reduction of Search Space in Restful Service Discovery

Web Services has been enabled IT services and computing technology to perform business services more efficiently and effectively. REpresentational State Transfer (REST) is to be used for creating Web APIs/services. In the existing system, web service search engines for RESTful Web Services/Api’s provide Keyword, Tag and Semantic based search functions. One of the RESTful service discovery, referred as Test-oriented RESTful service discovery with Semantic Interface Compatibility (TASSIC) have been developed by the search of RESTful Service’s/Api’s. TASSIC approach will search the semantic characteristics of search and match interface terms in the service document. An inability to consider the classification and in finding the suitable Api’s or services are a key issue of the search space in Tassic. A new approach has proposed for reduction of the search space in restful service discovery to develop a k-Nearest Neighbor classification algorithm. it provide candidate services with ranking based on semantic similarity, and classifying of similar candidate services and service unit testing will be considered. This approach is meant for increasing search precision in the retrieval and quick search for classifying their RESTful services or Api according to user-defined criteria.

Approach for a Machine-Interpretable Provision of Standard Contents Using Welded Constructions as an Example

In order to meet the quality standards required in today's product development process, the designer must be able to draw on the knowledge contained in standards at all times. However, in today's digital work environment, these are usually only available in paper or PDF form. To support the designer during the product development process, a research project examine how knowledge from standards can be made available digitally and integrated into his working environment. This paper presents a concept with a RESTful service as a central knowledge base, which provides knowledge in the form of microservices. The implementation is carried out using welding assemblies as an example. To achieve the high-quality requirements and to implement them, the standard contents had to be prepared in a machine-interpretable and cross system way.

Payment Point Online Bank (PPOB) Mobile Hybrid dengan Koneksi Billers Berbasis HTTP dan RESTful Services untuk Usaha Mikro

Sebuah perusahaan memiliki sejumlah agen kios yang sehari-harinya berjualan pulsa dengan perangkat Electronic Data Capture (EDC). Perusahaan tersebut ingin meningkatkan penjualan dengan menambah variasi produk yang dapat dijual dengan cara yang sama yaitu menggunakan perangkat mobile secara online. Sayangnya untuk melakukan pembaruan terhadap aplikasi yang ada di EDC tidak mudah karena membutuhkan pemrograman secara khusus dan aplikasi tersebut harus dipasang ulang satu persatu. Sebuah perusahaan yang memiliki layanan switching penjualan pulsa, token listrik dan pembayaran tagihan (billers) memiliki fasilitas yang memungkinkan pelanggannya membangun aplikasi yang dapat bertransaksi secara online antar server (Host-to-Host/H2H). Fitur tersebut berbasis HTTP dan RESTful services yang memungkinkan pengembang aplikasi lebih fleksibel dengan bahasa pemrograman yang dipilihnya. Dalam penelitian ini akan dikembangkan sebuah aplikasi mobile hybrid yang memiliki koneksi billers menggunakan metode tersebut. Aplikasi mobile hybrid memungkinkan pengembang menambahkan fitur-fitur baru tanpa harus mengubah aplikasi yang ada di perangkat milik pengguna. Hal ini sangat menguntungkan karena produk pembayaran online semakin banyak sehingga penambahan fitur akan sering dilakukan. Selain itu arsitektur mobile hybrid dengan koneksi HTTP dan RESTful service juga dapat digunakan dalam kasus lain yang serupa di mana penyedia layanan menyediakan Application Programming Interface (API) yang berbasis HTTP dan RESTful services.