IMPROVING STUDENTS READING COMPREHENSION ON RECOUNT TEXT THROUGH COLLABORATIVE LEARNING OF SMK NEGERI 02 PONTIANAK

AbstractThe research was conducted based on the problems found in teaching and learning process. Students had problems in reading comprehension, especially in finding main ideas, understanding the meaning of word, details, reference, and inference in the text. The purpose of this research was to investigate how Collaborative Learning improved students’ ability in reading comprehension to the Tenth Grade Students of SMK Negeri 02 Pontianak. The research was conducted through Classroom Action Research in two cycles. The participants of this research were the tenth grade English teacher and 38 students in class X TAV. The researcher used observation and measurement test to collect the data. The researcher elaborated the result of observation checklist, field note and students’ test result in order to get the research findings. The results showed that students’ reading comprehension improved by implementing Collaborative Learning. Most of the students were engaged well in learning the material and implementing Collaborative Learning. They worked cooperatively in a group. They also could understand the vocabulary in the passage appropriately and determine the main idea, details and reference word properly. The researchers expected at least the students’ minimum score in reading comprehension was 80. The students’ individual score in comprehending the text had achieved the researcher’s expectation. In conclusion, Collaborative Learning improved students’ reading comprehension ability. Keyword: Reading Comprehension, Collaborative Learning, Recount Text

Developing Real Time Tracking of User Behavior, with Google Analytics for Mobile Phone Devices

Sony Mobile has a quite large internal user group with the purpose of investigating the usability of their mobile devices. The Telephony Domain was using among other techniques usability testing to evaluate the usability of their products. The performed conventional usability testing has its limitations e.g. the controlled test environment cannot fully represent real life setting and it’s very expensive in terms of time and resources. This ultimately results in less test persons and potentially biased results. These drawbacks cannot be overlooked when it comes to determining the next software release influencing millions of mobile device users. The purpose of this thesis work was to accommodate this problem by examining real time tracking of user behavior and interaction with mobile devices. By utilizing Google Analytics in the Telephony Domain, we could autonomously gather large quantity of real user behavior data from a natural environment. The investigation resulted in the conclusion that Google Analytics & Google Tag Manager solely weren’t sufficient for our purposes in aiding information for user behavior. To account for this, a tool were developed that were to be called Usage Tracker. Usage Tracker works as a complement to Google Analytics & Google Tag Manager by providing further functionality e.g. finding out how many users are using a feature and how these events are distributed over the users. The resulting statistics from Usage Tracker is also presented in a more intuitive way for easy interpretation. Furthermore, a direct consequence of using Usage Tracker is that less data traffic will be required.Sony Mobile has a quite large internal user group with the purpose of investigating the usability of their mobile devices. The Telephony Domain was using among other techniques usability testing to evaluate the usability of their products. The performed conventional usability testing has its limitations e.g. the controlled test environment cannot fully represent real life setting and it’s very expensive in terms of time and resources. This ultimately results in less test persons and potentially biased results. These drawbacks cannot be overlooked when it comes to determining the next software release influencing millions of mobile device users. The purpose of this thesis work was to accommodate this problem by examining real time tracking of user behavior and interaction with mobile devices. By utilizing Google Analytics in the Telephony Domain, we could autonomously gather large quantity of real user behavior data from a natural environment. The investigation resulted in the conclusion that Google Analytics & Google Tag Manager solely weren’t sufficient for our purposes in aiding information for user behavior. To account for this, a tool were developed that were to be called Usage Tracker. Usage Tracker works as a complement to Google Analytics & Google Tag Manager by providing further functionality e.g. finding out how many users are using a feature and how these events are distributed over the users. The resulting statistics from Usage Tracker is also presented in a more intuitive way for easy interpretation. Furthermore, a direct consequence of using Usage Tracker is that less data traffic will be required

A structured annotation frame for the transposable phages: A new proposed family “Saltoviridae” within the Caudovirales

AbstractEnterobacteriophage Mu is the best studied and paradigm member of the transposable phages. Mu-encoded proteins have been annotated in detail in UniProtKB and linked to a controlled vocabulary describing the various steps involved in the phage lytic and lysogenic cycles.Transposable phages are ubiquitous temperate bacterial viruses with a dsDNA linear genome. Twenty-six of them, that infect α, β and γ-proteobacteria, have been sequenced. Their conserved properties are described. Based on these characteristics, we propose a reorganization of the Caudovirales, to allow for the inclusion of a “Saltoviridae” family and two newly proposed subfamilies, the “Myosaltovirinae” and “Siphosaltovirinae”. The latter could temporarily be included in the existing Myoviridae and Siphoviridae families

ViralZone: a knowledge resource to understand virus diversity

The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion picture

PeroxiBase: a database with new tools for peroxidase family classification

Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. They use various peroxides as electron acceptors to catalyse a number of oxidative reactions and are present in almost all living organisms. We have created a peroxidase database (http://peroxibase.isb-sib.ch) that contains all identified peroxidase-encoding sequences (about 6000 sequences in 940 organisms). They are distributed between 11 superfamilies and about 60 subfamilies. All the sequences have been individually annotated and checked. PeroxiBase can be consulted using six major interlink sections ‘Classes', ‘Organisms', ‘Cellular localisations', ‘Inducers', ‘Repressors' and ‘Tissue types'. General documentation on peroxidases and PeroxiBase is accessible in the ‘Documents' section containing ‘Introduction', ‘Class description', ‘Publications' and ‘Links'. In addition to the database, we have developed a tool to classify peroxidases based on the PROSITE profile methodology. To improve their specificity and to prevent overlaps between closely related subfamilies the profiles were built using a new strategy based on the silencing of residues. This new profile construction method and its discriminatory capacity have been tested and validated using the different peroxidase families and subfamilies present in the database. The peroxidase classification tool called PeroxiScan is accessible at the following address: http://peroxibase.isb-sib.ch/peroxiscan.ph

ProRule: a new database containing functional and structural information on PROSITE profiles

Motivation: Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. Summary: We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains. Availability: ProRule can be accessed through ScanProsite at http://www.expasy.org/tools/scanprosite. A file containing the rules will be made available under the PROSITE copyright conditions on our ftp site (ftp://www.expasy.org/databases/prosite/) by the next PROSITE release. Contact: [email protected]

PROSITE, a protein domain database for functional characterization and annotation

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 (∼70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/

New and continuing developments at PROSITE.

PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule a collection of rules, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRules

ViralZone: recent updates to the virus knowledge resource

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein record

New and continuing developments at PROSITE

PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule a collection of rules, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRule