chemf : a purely functional chemistry toolkit

Background: Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results: We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions: We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project

Identification of Design Principles

This report identifies those design principles for a (possibly new) query and transformation language for the Web supporting inference that are considered essential. Based upon these design principles an initial strawman is selected. Scenarios for querying the Semantic Web illustrate the design principles and their reflection in the initial strawman, i.e., a first draft of the query language to be designed and implemented by the REWERSE working group I4

The modern landscape of managing effects for the working programmer

The management of side effects is a crucial aspect of modern programming, especially in concurrent and distributed systems. This thesis analyses different approaches for managing side effects in programming languages, specifically focusing on unrestricted side effects, monads, and algebraic effects and handlers. Unrestricted side effects, used in mainstream imperative programming languages, can make programs difficult to reason about. Monads offer a solution to this problem by describing side effects in a composable and referentially transparent way but many find them cumbersome to use. Algebraic effects and handlers can address some of the shortcomings of monads by providing a way to model effects in more modular and flexible way. The thesis discusses the advantages and disadvantages of each of these approaches and compares them based on factors such as expressiveness, safety, and constraints they place on how programs must be implemented. The thesis focuses on ZIO, a Scala library for concurrent and asynchronous programming, which revolves around a ZIO monad with three type parameters. With those three parameters ZIO can encode the majority of practically useful effects in a single monad. ZIO takes inspiration from algebraic effects, combining them with monadic effects. The library provides a range of features, such as declarative concurrency, error handling, and resource management. The thesis presents examples of using ZIO to manage side effects in practical scenarios, highlighting its strengths over other approaches. The applicability of ZIO is evaluated by implementing a server side application using ZIO, and analyzing observations from the development process

Towards a Rule Interchange Language for the Web

This articles discusses rule languages that are needed for a a full deployment of the SemanticWeb. First, it motivates the need for such languages. Then, it presents ten theses addressing (1) the rule and/or logic languages needed on the Web, (2) data and data processing, (3) semantics, and (4) engineering and rendering issues. Finally, it discusses two options that might be chosen in designing a Rule Interchange Format for the Web

Accommodating prepositional phrases in a highly modular natural language query interface to semantic web triplestores using a novel event-based denotational semantics for English and a set of functional parser combinators

The SemanticWeb is an emerging component of the set of technologies that will be known as Web 3.0 in the future. With the large changes it brings to how information is stored and represented to users, there is a need to re-evaluate how this information can be queried. Specifically, there is a need for Natural Language Interfaces that allow users to easily query for information on the Semantic Web. While there has been previous work in this area, existing solutions suffer from the problem that they do not support prepositional phrases in queries (e.g, “in 1958” or “with a key”). To achieve this, we improve on an existing semantics for event-based triplestores that supports prepositional phrases and demonstrate a novel method of handling the word “by”, treating it directly as a preposition in queries. We then show how this new semantics can be integrated with a parser constructed as an executable attribute grammar to create a highly modular and extensible Natural Language Interface to the Semantic Web that supports prepositional phrases in queries

Towards a typology of coordinating compounds in Turkish

https://www.degruyter.com/view/j/flin.2018.52.issue-2/flin-2018-0008/flin-2018-0008.xml?format=IN

CyBy2 : a strongly typed, purely functional framework for chemical data management

We present the development of CyBy2, a versatile framework for chemical data management written in purely functional style in Scala, a modern multi-paradigm programming language. Together with the core libraries we provide a fully functional example implementation of a HTTP server together with a single page web client with powerful querying and visualization capabilities, providing essential functionality for people working in the field of organic and medicinal chemistry. The main focus of CyBy2 are the diverse needs of different research groups in the field and therefore the flexibility required from the underlying data model. Techniques for writing type level specifications giving strong guarantees about the correctness of the implementation are described, together with the resulting gain in confidence during refactoring. Finally we talk about the advantages of using a single code base from which the server, the client and the software's documentation pages are being generated. We conclude with a comparison with existing open source solutions. All code described in this article is published under version 3 of the GNU General Public License and available from GitHub including an example implementation of both backend and frontend together with documentation how to download and compile the software (available at https://github.com/stefan-hoeck/cyby2)