Generic API Research Articles

RuMono: Fuzz Driver Synthesis for Rust Generic APIs

Fuzzing is a popular technique for detecting bugs, which can be extended to libraries by constructing executables that call library APIs, known as fuzz drivers. Automated fuzz driver synthesis has been an important research topic in recent years since it can facilitate the library fuzzing process. Nevertheless, existing approaches generally ignore generic APIs or simply treat them as non-generic APIs. As a result, they cannot generate effective fuzz drivers for generic APIs. This paper explores the challenge of automating fuzz driver synthesis for Rust libraries with generic APIs. The problem is essential because Rust prioritizes security and generic APIs are widely employed in Rust libraries. We propose a novel approach and develop a prototype, RuMono, to tackle the problem. Our approach initially infers the API reachability from the generic API dependency graph, discovering the reachable and valid monomorphic APIs within the library. Further, we apply a similarity-based filter to eliminate redundant monomorphic APIs. Experimental results from 29 popular open-source libraries demonstrate that RuMono can achieve promising generic API coverage with a low rate of invalid fuzz drivers. Besides, we have identified 23 previously unknown bugs in these libraries, with 18 related to generic APIs.

Progress with Repository-based Annotation Infrastructure for Biodiversity Applications

Progress with Repository-based Annotation Infrastructure for Biodiversity Applications

CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering.

Density-based clustering procedures are widely used in a variety of data science applications. Their advantage lies in the capability to find arbitrarily shaped and sized clusters and robustness against outliers. In particular, they proved effective in the analysis of molecular dynamics simulations, where they serve to identify relevant, low-energetic molecular conformations. As such, they can provide a convenient basis for the construction of kinetic (core-set) Markov-state models. Here we present the open-source Python project CommonNNClustering, which provides an easy-to-use and efficient reimplementation of the common-nearest-neighbor (CommonNN) method. The package provides functionalities for hierarchical clustering and an evaluation of the results. We put our emphasis on a generic API design to keep the implementation flexible and open for customization.

High-performance symbolic-numerics via multiple dispatch

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. Exploiting this feature, we demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We illustrate how this symbolic system improves numerical computing tasks by showcasing an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

LoopStructural 1.0: time-aware geological modelling

Abstract. In this contribution we introduce LoopStructural, a new open-source 3D geological modelling Python package (http://www.github.com/Loop3d/LoopStructural, last access: 15 June 2021). LoopStructural provides a generic API for 3D geological modelling applications harnessing the core Python scientific libraries pandas, numpy and scipy. Six different interpolation algorithms, including three discrete interpolators and 3 polynomial trend interpolators, can be used from the same model design. This means that different interpolation algorithms can be mixed and matched within a geological model allowing for different geological objects, e.g. different conformable foliations, fault surfaces and unconformities to be modelled using different algorithms. Geological features are incorporated into the model using a time-aware approach, where the most recent features are modelled first and used to constrain the geometries of the older features. For example, we use a fault frame for characterising the geometry of the fault surface and apply each fault sequentially to the faulted surfaces. In this contribution we use LoopStructural to produce synthetic proof of concepts models and a 86 km × 52 km model of the Flinders Ranges in South Australia using map2loop.

STAGER: Semantic-Based Framework for Generating Adapters of Service-Based Generic-API for Portable Cloud Applications

In PaaS model, providers have different proprietary APIs, which make developers locked inside a specific platform and not able to easily port their applications among different platforms. So, vendor lock-in problem appeared. One solution to this problem is to use generic APIs with specific adapters. However, any update in a PaaS specific-API makes its corresponding adapter is unusable which causes, what we call, API synchronization problem. Therefore, STAGER (SemanTic-based GenERation of Generic-API Adapters) framework is proposed. STAGER framework provides a semi-automatic adapter generation process, which generates specific adapters of generic APIs for PaaS services (e.g., blob storage and datastore services) for target PaaS platforms. The adapter generation process is based on semantic annotations of the generic APIs and their corresponding PaaS specific-APIs. In order to evaluate STAGER framework, two generic APIs for blob storage and NoSQL datastore services have been proposed. STAGER framework is used to generate the adapters of these generic APIs for two PaaS platforms: Google App Engine (GAE) and Windows Azure. Although there is some overhead for semantically annotating the PaaS APIs, the evaluation results prove the feasibility of STAGER framework and promote the usage of the generated adapters for implementing portable cloud applications.

Development of Generic Drug Products by Pharmaceutical Industries Considering Regulatory Aspects: A Review

Development of generic drug product by pharmaceutical industry is a scientific and technical approach which is totally different from developing a reference or innovator product. Most of the developing countries focus on developing the generic drug products because huge amount of investment is required for innovation and to develop reference product. The generic medicine has to be bioequivalent to the innovator drug and ensure the same biological effect with proper safety and efficacy. Nowadays, the pharmaceutical industries focus on the development of generic product as this does not require that much time and cost compared to the innovator company. But development of generic product is also difficult as it contains the same therapeutic efficacy as innovator. The development approach is based on the target market, i.e. US market, EU market. If a manufacturer targets the US market, then all excipients should be USP grade, analysis should be conducted by USP method or in-house method and stability studies as well. Prior and during the development of generic drug product API selection, dosage form selection, reference product selection and characterization, formulation development, analytical method development, tech transfer or submission batch are prime concern. Then again, bioequivalence study, drug registration procedure and commercialization of the generic product considering regulatory guidance of respective regulatory agencies and the approaches taken by the regulatory agencies for the development of registration of generic medicines are also crucial as well for the development of generic drug product. The aim of this study was to review the entire stage of a generic drug development by a generic pharmaceutical company.

Trustful ad hoc cross‐organizational data exchanges based on the Hyperledger Fabric framework

SummaryOrganizations share data in a cross‐organizational context when they have the goal to derive additional knowledge by aggregating different data sources. The collaborations considered in this article are short‐lived and ad hoc, that is, they should be set up in a few minutes at most (e.g., in emergency scenarios). The data sources are located in different domains and are not publicly accessible. When a collaboration is finished, it is however unclear which exchanges happened. This could lead to possible disputes when dishonest organizations are present. The receipt of requests/responses could be falsely denied or their content could be point of discussion. In order to prevent such disputes afterwards, a logging mechanism is needed which generates a replicated irrefutable proof of which exchanges have happened during a single collaboration. Distributed database solutions can be taken from third parties to store the generated logs, but it can be difficult to find a party which is trusted by all participating organizations. Permissioned blockchains provide a solution for this as each organization can act as a consensus participant. Although the consensus mechanism of the permissioned blockchain Hyperledger Fabric (versions 1.0–1.4) is not fully decentralized, which clashes with the fundamental principle of blockchain, the framework is used in this article as an enabler to set up a distributed database, and a proposal for a logging mechanism is presented which does not require the third party to be fully trusted. A proof of concept is implemented which can be used to experiment with different data exchange setups. It makes use of generic web APIs and behaves according to a Markov chain in order to create a fully automated data exchange scenario where the participants explore their APIs dynamically. The resulting mechanism allows a data‐delivering organization to detect missing logs and to take action, for example, (temporarily) suspend collaboration. Furthermore, each organization is incentivized to follow the steps of the logging mechanism as it may lose access to data of others, otherwise. The created proof of concept is scaled to 10 organizations, which autonomously exchange different data types for 10 min, and evaluation results are presented accordingly.

Computer algebra with Rings library

Implementation of modern algorithms in computer algebra requires the use of generic and high-performance instruments. Rings is an open-source library, written in Java and Scala programming languages, which implements basic concepts and algorithms from computational commutative algebra while demonstrating quite a high performance among existing software. It rigorously uses generic programming approach, providing a well-designed generic API with a fully typed hierarchy of algebraic structures and algorithms for commutative algebra. Polynomial arithmetic, GCDs, factorization, and Gröbner bases are implemented with the use of modern asymptotically fast algorithms. The use of the Scala language brings a quite novel powerful, strongly typed functional programming model allowing to write short, expressive, and fast code for applications in high-energy physics and other research areas.

Generating a Generic Fluent API in Java

Context: The algorithms for generating a safe fluent API are actively studied these years. A safe fluent API is the fluent API that reports incorrect chaining of the API methods as a type error to the API users. Although such a safe property improves the productivity of its users, the construction of a safe fluent API is too complicated for the developers. The generation algorithms are studied to reduce the development cost of a safe fluent API. The study on the generation would benefit a number of programmers since a fluent API is a popular design in the real world. Inquiry: The generation of a generic fluent API has been left untackled. A generic fluent API refers to the fluent API that provides generic methods (methods that contain type parameters in their definitions). The Stream API in Java is an example of such a generic API. The recent research on the safe fluent API generation rather focuses on the grammar class that the algorithm can deal with for syntax checking. The key idea of the previous study is to use nested generics to represent a stack structure for the parser built on top of the type system. In that idea, the role of a type parameter was limited to internally representing a stack element of that parser on the type system. The library developers could not use type parameters to include a generic method in their API so that the semantic constraints for their API would be statically checked, for example, the type constraint on the items passed through a stream. Approach: We propose an algorithm to generate a generic fluent API. Our translation algorithm is modeled as the construction of deterministic finite automaton (DFA) with type parameter information. Each state of the DFA holds information about which type parameters are already bound in that state. This information is used to identify whether a method invocation in a chain newly binds a type to a type parameter, or refers to a previously bound type. The identification is required since a type parameter in a chain is bound at a particular method invocation, and that bound type is referred to in the following method invocations. Our algorithm constructs the DFA by analyzing the binding time of type parameters and their propagation among the states in a DFA that is naively constructed from the given grammar. Knowledge and Importance: Our algorithm helps library developers to develop a generic fluent API. The ability to generate a generic fluent API is essential to bring the safe fluent API generation to the real world since the use of type parameters is a common technique in the library API design. By our algorithm, the generation of a safe fluent API will be ready for practical use. Grounding: We implemented a generator named Protocool to demonstrate our algorithm. We also generated several libraries using Protocool to show the ability and the limitations of our algorithm.

Regulatory Challenges of Sterile Formulation Development As Per USFDA Prospectives

For the sterile product development FDA has taken many initiatives for the safety and efficacious products. Recently, many works have been done for the improvement in drug development. Quality by Design (QBD) Product and manufacturing process development, as well as safe use and product design, are among the elements of enhanced technical involvement. In this review, we discussed an overview of regulatory challenges to improve the quality aspects for sterile drugs. FDA has regulated current good manufacturing practice (CGMP) regulations for the manufacture of large volume parenterals. The studies can then be prolonged to multiple ingredients to assure compatibility with the API and each of the excipients. The compatibility of the drug product should provide appropriate information about the drug product. It should deals with the quality of drug product and route of administration for the intended use. Microbiological review conducted in 1970–1971 for the manufacture of sterile drug was one of FDA's responses to the nosocomial bacteremias, Recently the new drug microbiology review function has been re-examining its role in non-sterile dosage forms in order to Know about recalls and adverse event for oral and topical drug products. For the Active pharmaceutical ingredient justifying the quality source is generally time-consuming effort whether the product is manufacturein-house, as with an Non chemical entity, or sourced externally, as with a generic API.5

HyPar: A divide-and-conquer model for hybrid CPU–GPU graph processing

Efficient processing of graph applications on heterogeneous CPU–GPU systems require effectively harnessing the combined power of both the CPU and GPU devices. This paper presents HyPar, a divide-and-conquer model for processing graph applications on hybrid CPU–GPU systems. Our strategy partitions the given graph across the devices and performs simultaneous independent computations on both the devices. The model provides a simple and generic API, supported with efficient runtime strategies for hybrid executions. The divide-and-conquer model is demonstrated with five graph applications and using experiments with these applications on a heterogeneous system it is shown that our HyPar strategy provides equivalent performance to the state-of-art, optimized CPU-only and GPU-only implementations of the corresponding applications. When compared to the prevalent BSP approach for multi-device executions of graphs, our HyPar method yields 74%–92% average performance improvements.

A novel two-dimensional liquid chromatography - Mass spectrometry method for direct drug impurity identification from HPLC eluent containing ion-pairing reagent in mobile phases

In this study, a novel two dimensional liquid chromatography – mass spectrometry (2D-LC-MS) method with use of a weak anion exchange column between the 1st DLC RP column and the 2nd DLC RP column (RP1-WAX-RP2) was developed and applied to identify drug impurities from MS incompatible mobile phases containing sodium 1-octanesulfonate and non-volatile buffer. The 1st DLC conditions follow exactly the original standard HPLC method recorded in Chinese Pharmacopeia (ChP), European Pharmacopeia (EP) or US Pharmacopeia (USP). An impurity fraction was collected with a built-in sample loop (100 μL) and transferred to the WAX column where 1-octanesulfonate and phosphate were trapped and removed. While, the impurity and other cations were eluted to the 2nd D column (RP2) for separation and identification by connected IT-TOF MS. Methods were programmed and applied to identify impurities in two generic drugs, sulpiride (hydrophilic drug with logP 0.57) and dobutamine (hydrophobic drug with logP 3.6). The results indicate that the methods based on RP1-WAX-RP2 column configuration offer a feasible solution for direct impurity identification in generic drug product or API without needs of off-line desalting from the MS incompatible mobile phases containing ion-pairing reagent and non-volatile buffer.

HPC Process and Optimal Network Device Affinitization

High Performance Computing (HPC) applications have demanding need for hardware resources such as processor, memory, and storage. Applications in the area of Artificial Intelligence and Machine Learning are taking center stage in HPC, which is driving demand for increasing compute resources per node which in turn is pushing bandwidth requirement between the compute nodes. New system design paradigms exist where deploying a system with more than one high performance IO device per node provides benefits. The number of I/O devices connected to the HPC node can be increased with PCIe switches and hence some of the HPC nodes are designed to include PCIe switches to provide a large number of PCIe slots. With multiple IO devices per node, application programmers are forced to consider HPC process affinity to not only compute resources but extend this to include IO devices. Mapping of process to processor cores and the closest IO device(s) increases complexity due to three way mapping and varying HPC node architectures. While operating systems perform reasonable mapping of process to processor core(s), they lack the application developer's knowledge of process workflow and optimal IO resource allocation when more than one IO device is attached to the compute node. This paper is an extended version of our work published in [1] . Our previous work provided solution for IO device affinity choices by abstracting the device selection algorithm from HPC applications. In this paper, we extend the affinity solution to enable OpenFabric Interfaces (OFI) which is a generic HPC API designed as part of the OpenFabrics Alliance that enables wider HPC programming models and applications supported by various HPC fabric vendors. We present a solution for IO device affinity choices by abstracting the device selection algorithm from HPC applications. MPI continues to be the dominant programming model for HPC and hence we provide evaluation with MPI based micro benchmarks. Our solution is then extended to OpenFabric Interfaces which supports other HPC programming models such as SHMEM, GASNet, and UPC. We propose a solution to solve NUMA issues at the lower level of the software stack that forms the runtime for MPI and other programming models independent of HPC applications. Our experiments are conducted on a two node system where each node consists of two socket Intel Xeon servers, attached with up to four Intel Omni-Path fabric devices connected over PCIe. The performance benefits seen by applications by affinitizing processes with best possible network device is evident from the results where we notice up to 40 percent improvement in uni-directional bandwidth, 48 percent bi-directional bandwidth, 32 percent improvement in latency measurements, and up to 40 percent improvement in message rate with OSU benchmark suite. We also extend our evaluation to include OFI operations and an MPI benchmark used for Genome assembly. With OFI Remote Memory Access (RMA) operations we see a bandwidth improvement of 32 percent for fi_read and 22 percent with fi_write operations, and also latency improvement of 15 percent for fi_read and 14 percent for fi_write. K-mer MMatching Interface HASH benchmark shows an improvement of up to 25 percent while using local network device versus using a network device connected to remote Xeon socket.

The BIG IoT API - Semantically Enabling IoT Interoperability

Today, internet of things (IoT) platforms offer proprietary interfaces and protocols. To enable interoperable interaction with those platforms we present the generic BIG IoT API that employs a novel approach for self-description and semantic annotation to fully adapt arbitrary IoT platforms. We have deployed this approach for multiple platforms from the mobility domain.

A high‐level library for multidimensional arrays programming in computational science

SummaryThis paper describes ExaShark, a hybrid n‐dimensional array toolkit offered as a high‐level library for scientists to compute large‐scale simulations. It offers a global‐array–like interface while its runtime can be configured to use shared memory threading techniques, inter‐node distribution techniques, or combinations of both. ExaShark takes advantage of the latest HPC technologies, helping to scale to future generation systems. It has been used to develop several scientific applications including stencil codes, solvers, and matrix factorization algorithms. These applications are used to demonstrate that it improves on the state of the art by providing a user‐friendly, generic API without sacrificing performance.

In Search of Suitable Transfer Pricing Method for Active Pharmaceutical Ingredients – A Case of Pakistan

This article is concerned with finding an appropriate transfer pricing method for determining the arm’s length price of active pharmaceutical ingredients (APIs in related-party transactions). It examines the available transfer pricing methods and sets out the appropriateness of each method for a particular type of transaction. Further, this article reviews pharmacology literature for the comparison of innovator and generic APIs and it also reviews commonly cited case law from selected developed jurisdictions and from Pakistan.

Towards standard PaaS implementation APIs

Platform as a service (PaaS) supports application developers with the ability to implement and deploy their applications in the cloud. Several heterogeneous PaaS platforms are available, such as Google App Engine (GAE), Windows Azure, Cloud Foundry, and OpenShift. Each PaaS provider has its own proprietary implementation and deployment APIs. The heterogeneity of these APIs makes developers worry about their application portability and interoperability. The work in this paper concerns about the heterogeneity of different PaaS implementation APIs. Standard PaaS implementation APIs, called Std-PaaS APIs, have been proposed to solve the application portability problem. Std-PaaS APIs allow developers to develop generic cloud application by writing their applications once and deploying many times on heterogeneous PaaS providers. Std-PaaS APIs have been evaluated using two case studies, in which generic APIs for cloud persistentstorage service and NoSQL datastore service have been developed and used to developed applications to be deployed onto GAE and Windows Azure.

Towards standard PaaS implementation APIs

Platform as a service (PaaS) supports application developers with the ability to implement and deploy their applications in the cloud. Several heterogeneous PaaS platforms are available, such as Google App Engine (GAE), Windows Azure, Cloud Foundry, and OpenShift. Each PaaS provider has its own proprietary implementation and deployment APIs. The heterogeneity of these APIs makes developers worry about their application portability and interoperability. The work in this paper concerns about the heterogeneity of different PaaS implementation APIs. Standard PaaS implementation APIs, called Std-PaaS APIs, have been proposed to solve the application portability problem. Std-PaaS APIs allow developers to develop generic cloud application by writing their applications once and deploying many times on heterogeneous PaaS providers. Std-PaaS APIs have been evaluated using two case studies, in which generic APIs for cloud persistentstorage service and NoSQL datastore service have been developed and used to developed applications to be deployed onto GAE and Windows Azure.

Towards a Generic BPMS User Portal Definition for the Execution of Business Processes

Business Process Management Systems (BPMS) provide support for the business process (BPs) lifecycle, from modeling to executing and evaluating BPs. Key elements provided within a BPMS are a process engine where BP models are executed and a web portal for user's interaction providing means to manage a work list, taking and completing tasks, among other functionalities. Most BPMS portals provide a set of core features for users to manage their work lists, as well as service-oriented access to their process engine, which is tightly coupled. In this context it seems possible to define a generic BPMS user portal which can be integrated (loosely coupled) with potentially any process engine for the execution of business processes. In this paper we define such generic BPMS user portal based on a unified data model and a generic process engine API. We also show the feasibility of these ideas through the development of a prototype.