Using R and Bioconductor for proteomics data analysis.

This review presents how R, the popular statistical environment and programming language, can be used in the frame of proteomics data analysis. A short introduction to R is given, with special emphasis on some of the features that make R and its add-on packages premium software for sound and reproducible data analysis. The reader is also advised on how to find relevant R software for proteomics. Several use cases are then presented, illustrating data input/output, quality control, quantitative proteomics and data analysis. Detailed code and additional links to extensive documentation are available in the freely available companion package RforProteomics. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan

Methodological approaches and techniques for designing ontologies in information systems requirements engineering

Programa doutoral em Information Systems and TechnologyThe way we interact with the world around us is changing as new challenges arise, embracing innovative business models, rethinking the organization and processes to maximize results, and evolving change management. Currently, and considering the projects executed, the methodologies used do not fully respond to the companies' needs. On the one hand, organizations are not familiar with the languages used in Information Systems, and on the other hand, they are often unable to validate requirements or business models. These are some of the difficulties encountered that lead us to think about formulating a new approach. Thus, the state of the art presented in this paper includes a study of the models involved in the software development process, where traditional methods and the rivalry of agile methods are present. In addition, a survey is made about Ontologies and what methods exist to conceive, transform, and represent them. Thus, after analyzing some of the various possibilities currently available, we began the process of evolving a method and developing an approach that would allow us to design ontologies. The method we evolved and adapted will allow us to derive terminologies from a specific domain, aggregating them in order to facilitate the construction of a catalog of terminologies. Next, the definition of an approach to designing ontologies will allow the construction of a domain-specific ontology. This approach allows in the first instance to integrate and store the data from different information systems of a given organization. In a second instance, the rules for mapping and building the ontology database are defined. Finally, a technological architecture is also proposed that will allow the mapping of an ontology through the construction of complex networks, allowing mapping and relating terminologies. This doctoral work encompasses numerous Research & Development (R&D) projects belonging to different domains such as Software Industry, Textile Industry, Robotic Industry and Smart Cities. Finally, a critical and descriptive analysis of the work done is performed, and we also point out perspectives for possible future work.A forma como interagimos com o mundo à nossa volta está a mudar à medida que novos desafios surgem, abraçando modelos empresariais inovadores, repensando a organização e os processos para maximizar os resultados, e evoluindo a gestão da mudança. Atualmente, e considerando os projetos executados, as metodologias utilizadas não respondem na totalidade às necessidades das empresas. Por um lado, as organizações não estão familiarizadas com as linguagens utilizadas nos Sistemas de Informação, por outro lado, são muitas vezes incapazes de validar requisitos ou modelos de negócio. Estas são algumas das dificuldades encontradas que nos levam a pensar na formulação de uma nova abordagem. Assim, o estado da arte apresentado neste documento inclui um estudo dos modelos envolvidos no processo de desenvolvimento de software, onde os métodos tradicionais e a rivalidade de métodos ágeis estão presentes. Além disso, é efetuado um levantamento sobre Ontologias e quais os métodos existentes para as conceber, transformar e representar. Assim, e após analisarmos algumas das várias possibilidades atualmente disponíveis, iniciou-se o processo de evolução de um método e desenvolvimento de uma abordagem que nos permitisse conceber ontologias. O método que evoluímos e adaptamos permitirá derivar terminologias de um domínio específico, agregando-as de forma a facilitar a construção de um catálogo de terminologias. Em seguida, a definição de uma abordagem para conceber ontologias permitirá a construção de uma ontologia de um domínio específico. Esta abordagem permite em primeira instância, integrar e armazenar os dados de diferentes sistemas de informação de uma determinada organização. Num segundo momento, são definidas as regras para o mapeamento e construção da base de dados ontológica. Finalmente, é também proposta uma arquitetura tecnológica que permitirá efetuar o mapeamento de uma ontologia através da construção de redes complexas, permitindo mapear e relacionar terminologias. Este trabalho de doutoramento engloba inúmeros projetos de Investigação & Desenvolvimento (I&D) pertencentes a diferentes domínios como por exemplo Indústria de Software, Indústria Têxtil, Indústria Robótica e Smart Cities. Finalmente, é realizada uma análise critica e descritiva do trabalho realizado, sendo que apontamos ainda perspetivas de possíveis trabalhos futuros

Data-Juicer: A One-Stop Data Processing System for Large Language Models

The immense evolution in Large Language Models (LLMs) has underscored the importance of massive, diverse, and high-quality data. Despite this, existing open-source tools for LLM data processing remain limited and mostly tailored to specific datasets, with an emphasis on the reproducibility of released data over adaptability and usability, inhibiting potential applications. In response, we propose a one-stop, powerful yet flexible and user-friendly LLM data processing system named Data-Juicer. Our system offers over 50 built-in versatile operators and pluggable tools, which synergize modularity, composability, and extensibility dedicated to diverse LLM data processing needs. By incorporating visualized and automatic evaluation capabilities, Data-Juicer enables a timely feedback loop to accelerate data processing and gain data insights. To enhance usability, Data-Juicer provides out-of-the-box components for users with various backgrounds, and fruitful data recipes for LLM pre-training and post-tuning usages. Further, we employ multi-facet system optimization and seamlessly integrate Data-Juicer with both LLM and distributed computing ecosystems, to enable efficient and scalable data processing. Empirical validation of the generated data recipes reveals considerable improvements in LLaMA performance for various pre-training and post-tuning cases, demonstrating up to 7.45% relative improvement of averaged score across 16 LLM benchmarks and 16.25% higher win rate using pair-wise GPT-4 evaluation. The system's efficiency and scalability are also validated, supported by up to 88.7% reduction in single-machine processing time, 77.1% and 73.1% less memory and CPU usage respectively, and 7.91x processing acceleration when utilizing distributed computing ecosystems. Our system, data recipes, and multiple tutorial demos are released, calling for broader research centered on LLM data.Comment: Under continuous maintenance and updating; The system, refined data recipes, and demos are at https://github.com/alibaba/data-juice

ICSEA 2021: the sixteenth international conference on software engineering advances

The Sixteenth International Conference on Software Engineering Advances (ICSEA 2021), held on October 3 - 7, 2021 in Barcelona, Spain, continued a series of events covering a broad spectrum of software-related topics. The conference covered fundamentals on designing, implementing, testing, validating and maintaining various kinds of software. The tracks treated the topics from theory to practice, in terms of methodologies, design, implementation, testing, use cases, tools, and lessons learnt. The conference topics covered classical and advanced methodologies, open source, agile software, as well as software deployment and software economics and education. The conference had the following tracks: Advances in fundamentals for software development Advanced mechanisms for software development Advanced design tools for developing software Software engineering for service computing (SOA and Cloud) Advanced facilities for accessing software Software performance Software security, privacy, safeness Advances in software testing Specialized software advanced applications Web Accessibility Open source software Agile and Lean approaches in software engineering Software deployment and maintenance Software engineering techniques, metrics, and formalisms Software economics, adoption, and education Business technology Improving productivity in research on software engineering Trends and achievements Similar to the previous edition, this event continued to be very competitive in its selection process and very well perceived by the international software engineering community. As such, it is attracting excellent contributions and active participation from all over the world. We were very pleased to receive a large amount of top quality contributions. We take here the opportunity to warmly thank all the members of the ICSEA 2021 technical program committee as well as the numerous reviewers. The creation of such a broad and high quality conference program would not have been possible without their involvement. We also kindly thank all the authors that dedicated much of their time and efforts to contribute to the ICSEA 2021. We truly believe that thanks to all these efforts, the final conference program consists of top quality contributions. This event could also not have been a reality without the support of many individuals, organizations and sponsors. We also gratefully thank the members of the ICSEA 2021 organizing committee for their help in handling the logistics and for their work that is making this professional meeting a success. We hope the ICSEA 2021 was a successful international forum for the exchange of ideas and results between academia and industry and to promote further progress in software engineering research

Portuguese SKA white book

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Development of BIM implementation framework for digital construction in Tukey

Yapı Bilgi Modellemesi (BIM), bir binanın planlama, tasarım, inşaat ve işletme sürecini 3B ve ötesine entegre etmek için yenilikçi bir yaklaşımdır. Bu yenilikçi yaklaşım ülkemizde henüz istenilen düzeye gelmemiştir. Gelişmiş ülkeler ise, inşaat sektörünü işci odaklı sektörden bilgiye dayalı bir sektöre dönüştürmek için bir takım stratejik politikalar izlemektedir. Son yıllarda, inşaat sektörü Türkiye'de ülke ekonomisinin öncü sektörlerinden birisi haline gelmiştir. Ancak, bu sektörde uygulanan geleneksel inşaat yöntemleri ve uygulamaları, verimliliği ve sürdürülebilirliği olumsuz yönde etkilemektedir. Dünya geneline baktığımızda yaygın olarak kullanılan BIM tabanlı proje tasarımı ve yönetimi Türkiye'de henüz istenilen düzeye ulaşamamıştır. Ayrıca, BIM tabanlı tasarım ve yapım yaklaşımının, Türkiye'deki endüstriyel üreticiler tarafından ortak bir kullanımı da yoktur. Bu neden ile dijital dönüşümün önündeki engellerin üstesinden gelmek ve endüstrinin BIM tabanlı uygulamaya geçişini hızlandırmak için uygulanabilir bir stratejik yol haritası hazırlanması gerekmektedir. Bu çalışma; dijital dönüşümün sosyal ve teknik yönleri, iş modeli, eğitim ve inşaat piyasasına entegrasyonu ve sürdürülebilirlik gibi temel unsurları incelemeyi amaçlarken, aynı zamanda, Türk inşaat sektöründe BIM kullanımının farkındalığının arttırılması, geçiş sürecinin doğru yönetilmesi ve engelleri sistematik bir şekilde ortadan kaldırmayı hedeflemektedir. Yaptığımız bu çalışmada, niteliksel ve niceliksel araştırma yöntemleri bir arada kullanılmıştır. Nitel veriler doküman incelemelerinden, gözlemlerden ve görüşmelerden elde edilirken, nicel veriler ise vaka çalışması analizlerinden ve ankete dayalı verilerden oluşmuştur. Araştırmada şimdiye kadar toplanan verilerin analizi, Türkiye'de BIM uygulama planının gelişmesinde büyük bir rol oynayacaktır. Son olarak bu çalışma içeriği ile etkinliklerle kapasite oluşturma, BIM standartları ve protokolleri geliştirme, üniversite eğitim sistemleri ile ilgili düzenlemeler, profesyoneller arasında bilgi paylaşımı süreçlerini gerçekleştirilmesini kapsar. Bu kapsam doğrultusunda, uygulama planını sistematik bir şekilde hayata geçirilmesi için BIM merkezine ihtiyaç vardır