FastaValidator: an open-source Java library to parse and validate FASTA formatted sequences

Background: Advances in sequencing technologies challenge the efficient importing and validation of FASTA formatted sequence data which is still a prerequisite for most bioinformatic tools and pipelines. Comparative analysis of commonly used Bio*-frameworks (BioPerl, BioJava and Biopython) shows that their scalability and accuracy is hampered. Findings: FastaValidator represents a platform-independent, standardized, light-weight software library written in the Java programming language. It targets computer scientists and bioinformaticians writing software which needs to parse quickly and accurately large amounts of sequence data. For end-users FastaValidator includes an interactive out-of-the-box validation of FASTA formatted files, as well as a non-interactive mode designed for high-throughput validation in software pipelines. Conclusions: The accuracy and performance of the FastaValidator library qualifies it for large data sets such as those commonly produced by massive parallel (NGS) technologies. It offers scientists a fast, accurate and standardized method for parsing and validating FASTA formatted sequence data

O ensino de PHP em páginas web dinâmicas através do desenvolvimento de um "fórum online sobre património cultural"

Relatório da Prática de Ensino Supervisionada, Mestrado em Ensino da Informática, Universidade de Lisboa, Instituto de Educação, 2020O presente relatório foi concretizado no âmbito da unidade curricular de Iniciação à Prática Profissional IV do Mestrado em Ensino da Informática do Instituto de Educação da Universidade de Lisboa. Retrata a intervenção pedagógica na Escola Secundária Gago Coutinho, numa turma do segundo ano do Curso Profissional de Técnico de Gestão e Programação de Sistemas Informáticos na disciplina de Redes de Comunicação e concretamente no final do módulo cinco: “Desenvolvimento de Páginas Web Dinâmicas” com a duração de catorze tempos letivos de quarenta e cinco minutos de prática de ensino supervisionada. Em virtude da suspensão das aulas presenciais por ordem do Governo a dezasseis de março de 2020 devido à pandemia COVID-19, quatro tempos decorreram presencialmente e dez tempos letivos decorreram à distância de forma síncrona via Zoom. Os conteúdos programáticos abordados foram os seguintes: sessões, cookies, tratamento de erros na linguagem PHP (PHP: Hypertext Preprocessor) e a consolidação de conhecimentos em linguagens PHP, HTML (Hyper Text Markup Language), CSS (Cascading Style Sheets) e SQL (Structured Query Language), que permitiram criar um fórum online sobre o património do concelho de Vila Franca de Xira que se enquadrou no tema do DAC (Domínio de Autonomia Curricular) da turma. Foi realizado um trabalho interdisciplinar e de articulação curricular privilegiando o trabalho prático e o desenvolvimento das capacidades de pesquisa, relação e análise, com vista ao desenvolvimento das áreas de competências inscritas no Perfil dos Alunos à Saída da Escolaridade Obrigatória. No decorrer da prática de ensino supervisionada foram usadas várias metodologias, nomeadamente a ativa, interrogativa e também a expositiva, de modo a minimizar as dificuldades identificadas por alguns autores no ensino dos princípios da programação aos alunos. Por fim, com o objetivo de avaliar de forma contínua as atitudes, o trabalho desenvolvido pelos alunos e a aquisição de conhecimentos, foram utilizadas ferramentas de avaliação diagnóstica, formativa e sumativa.The following report was accomplished in the curricular unit ambit of Initiation to Professional Practice IV Master’s Degree in Computer Science Teaching at Lisbon University, Educational Institute. The pedagogical intervention retracts the Secondary School Gago Coutinho, of an A-levels class from a Professional and Technical course in Management and Computer Systems Developer, considering the subject of communication networks, more precisely at the end of the 5th unit: “Dynamic Web Pages Development” the supervised teaching practice had the duration of 14 academic days which lasted 45 minutes each. Due to the COVID-19 pandemic, school suspension of presential classes was ordered by the government, March 16th of 2020, so only 4 academic days were attended. The remaining 10 occurred in long-distance learning synchronously using Zoom. The addressed programmatic contents were the following: sessions, cookies, language error treatment PHP (PHP: Hypertext Preprocessor) and knowledge in languages consolidation in PHP, HTML (HyperText Markup Language), CSS (Cascading Style Sheets) e SQL (Structured Query Language), which allowed to create an online forum about Vila Franca de Xira municipality Patrimony, and framed the theme CAD (Curricular Autonomy Dominance) of the class. An interdisciplinary work was carried out in the curricular articulation, privileging the practical work. Development of searching capabilities, relationship association, and analyse. Considering this, the intent is to develop the several knowledge areas enrolled in the student’s profile when they exit the obligatory schooling. During the practicing supervised taught, several methodologies were used. Such as active, interrogative, and expositive, to minimize the difficulties presented by some authors concerning teaching programming principal to students. To summarize, the objective is: To evaluate the attitudes continuously, the acquisition of knowledge, and work developed by the students. This became possible using tools of diagnostic, formative, and summative evaluation

Microbial community responses determine how soil–atmosphere exchange of carbonyl sulfide, carbon monoxide, and nitric oxide responds to soil moisture

Carbonyl sulfide (OCS) plays an important role in the global sulfur cycle and is relevant for climate change due to its role as a greenhouse gas, in aerosol formation and atmospheric chemistry. The similarities of the carbon dioxide (CO2) and OCS molecules within chemical and plant metabolic pathways have led to the use of OCS as a proxy for global gross CO2 fixation by plants (gross primary production, GPP). However, unknowns such as the OCS exchange from soils, where simultaneous OCS production (POCS) and consumption (UOCS) occur, currently limits the use of OCS as a GPP proxy. We estimated POCS and UOCS by measuring net fluxes of OCS, carbon monoxide (CO), and nitric oxide (NO) in a dynamic chamber system fumigated with air containing different mixing ratios [OCS]. Nine soils with different land use were rewetted and soil–air exchange was monitored as soils dried out to assess responses to changing moisture. A major control of OCS exchange was the total amount of available sulfur in the soil. POCS production rates were highest for soils at WFPS (water-filled pore space) &gt;60&thinsp;% and rates were negatively related to thiosulfate concentrations. These moist soils switched from a net source to a net sink activity at moderate moisture levels (WFPS 15&thinsp;% to 37&thinsp;%). For three soils we measured NO and CO mixing ratios at different mixing ratios of OCS and revealed that NO and potentially CO exchange rates are linked to UOCS at moderate soil moisture. High nitrate concentrations correlated with maximum OCS release rates at high soil moisture. For one of the investigated soils, the moisture and OCS mixing ratio was correlated with different microbial activity (bacterial 16S rRNA, fungal ITS RNA relative abundance) and gene transcripts of red-like cbbL and amoA.</p

First divertor physics studies in Wendelstein 7-X

The Wendelstein 7-X (W7-X) optimized stellarator fusion experiment, which went into operation in 2015, has been operating since 2017 with an un-cooled modular graphite divertor. This allowed first divertor physics studies to be performed at pulse energies up to 80 MJ, as opposed to 4 MJ in the first operation phase, where five inboard limiters were installed instead of a divertor. This, and a number of other upgrades to the device capabilities, allowed extension into regimes of higher plasma density, heating power, and performance overall, e.g. setting a new stellarator world record triple product. The paper focuses on the first physics studies of how the island divertor works. The plasma heat loads arrive to a very high degree on the divertor plates, with only minor heat loads seen on other components, in particular baffle structures built in to aid neutral compression. The strike line shapes and locations change significantly from one magnetic configuration to another, in very much the same way that codes had predicted they would. Strike-line widths are as large as 10 cm, and the wetted areas also large, up to about 1.5 m(2), which bodes well for future operation phases. Peak local heat loads onto the divertor were in general benign and project below the 10 MW m(-2) limit of the future water-cooled divertor when operated with 10 MW of heating power, with the exception of low-density attached operation in the high-iota configuration. The most notable result was the complete (in all 10 divertor units) heat-flux detachment obtained at high-density operation in hydrogen