Gestión de Procesos en los Sistemas Operativos

Comparación de los sistemas operativos Windows 7 Profesional, Ubuntu 10.10 Desktop y Mac OS X Snow Leopard Desktop respecto al rendimiento que ofrecen sobre el servidorweb Apache instalado en cada uno de ellos.

Anàlisi Dinàmic de programes "PinCloud"

Anàlisi dinàmic de programes mitjançant la PinTool mtaptrace a través d'un servei Web Server construït en llenguatge PHP i Bases de Dades SQL

Anàlisi, disseny i implementació d'una aplicació fent servir l'arquitectura J2EE

Aplicació basada en l'arquitectura J2EE. Amb la utilització del framework Struts 2, s'ha desenvolupat una aplicació web tenint com a base el patró Model - Vista - Controlador. Es detallen les diferents fases (estudi inicial, anàlisi funcional, disseny i implementació) per tal de realitzar el projecte: 'Accés i consulta de la informació relacionada amb un centre mèdic'.

SGP-1: prediction and validation of homologous genes based on sequence alignments

Conventional methods of gene prediction rely on the recognition of DNA-sequence signals, the coding potential or the comparison of a genomic sequence with a cDNA, EST, or protein database. Reasons for limited accuracy in many circumstances are species-specific training and the incompleteness of reference databases. Lately, comparative genome analysis has attracted increasing attention. Several analysis tools that are based on human/mouse comparisons are already available. Here, we present a program for the prediction of protein-coding genes, termed SGP-1 (Syntenic Gene Prediction), which is based on the similarity of homologous genomic sequences. In contrast to most existing tools, the accuracy of SGP-1 depends little on species-specific properties such as codon usage or the nucleotide distribution. SGP-1 may therefore be applied to nonstandard model organisms in vertebrates as well as in plants, without the need for extensive parameter training. In addition to predicting genes in large-scale genomic sequences, the program may be useful to validate gene structure annotations from databases. To this end, SGP-1 output also contains comparisons between predicted and annotated gene structures in HTML format. The program can be accessed via a Web server at http://soft.ice.mpg.de/sgp-1. The source code, written in ANSI C, is available on request from the authors.

MyHits: improvements to an interactive resource for analyzing protein sequences.

The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service. The MySQL schema and its associated API were revamped and the database engine (HitKeeper) was separated from the web interface. This paper summarizes the current status of the server, with an emphasis on the new services.

HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites.

HTPSELEX is a public database providing access to primary and derived data from high-throughput SELEX experiments aimed at characterizing the binding specificity of transcription factors. The resource is primarily intended to serve computational biologists interested in building models of transcription factor binding sites from large sets of binding sequences. The guiding principle is to make available all information that is relevant for this purpose. For each experiment, we try to provide accurate information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, assembled clone sequences (concatemers) and complete sets of in vitro selected protein-binding tags. In addition, we offer in-house derived binding sites models. HTPSELEX also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols. The FTP site contains the trace archives and database flatfiles. The web server offers user-friendly interfaces for viewing individual entries and quality-controlled download of SELEX sequence libraries according to a user-defined sequencing quality threshold. HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex.

The Microbe browser for comparative genomics.

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api.

Gestió de la informació d'interès d'un treballador autònom

L’objectiu principal d’aquest treball és fer un programa que permeti portar la informació que un treballador autònom li interessa, d’acord amb les seves necessitats. En el nostre cas es tracta d’un centre d’estètica, que té més d’una seu, el qual li interessa portar tota la cartilla de clients, centres associats, proveïdors ... a més de poder fer les factures corresponents als centres associats, poder calcular en el moment que en el treballador li interessi, els ingressos realitzats durant un període de temps determinat i poder portar una agenda actualitzada dels dos centres, on es mostren totes les visites que hi ha en un dia. Per tal de realitzar el programa, s’han portat a terme mitjançant dos aplicacions, i connectant-los en una base de dades. Per una banda tenim una aplicació implementada amb C++, per l’altra, una pàgina web amb PHP, finalment com a sistema gestor de base de dades utilitzem el MySQL Server. El programa fet amb C++, consta de tota la part d’entrada i/o modificacions de dades, en aquesta part només hi pot accedir el treballador autònom, ja que és la única persona que pot fer aquesta feina. En la pàgina web, hi pot accedir qualsevol persona que tingui un nom d’usuari i una contrasenya. A través de la web es pot fer qualsevol tipus de consulta, fer tot el control de les agendes, portar a terme tot el tema de facturació i ingressos, i com a excepció l’entrada de dades de clients, ja que s’ha de poder realitzar en qualsevol moment i lloc. Per acabar, tenim la necessitat de tenir un servidor, aquest ha d’estar format, mínim, per la base de dades. Com que l’aplicació amb C++ i la base de dades han d’estar ubicades al mateix lloc. A més, necessitem un servidor web per tal de tenir la nostra pàgina a la xarxa, per aconseguir això, utilitzem un programa anomenat DynDNS, que es fa servir per a convertir una IP dinàmica en una IP estàtica i d’aquesta manera convertir un ordinador qualsevol amb un servidor web.

Native homing endonucleases can target conserved genes in humans and in animal models.

In recent years, both homing endonucleases (HEases) and zinc-finger nucleases (ZFNs) have been engineered and selected for the targeting of desired human loci for gene therapy. However, enzyme engineering is lengthy and expensive and the off-target effect of the manufactured endonucleases is difficult to predict. Moreover, enzymes selected to cleave a human DNA locus may not cleave the homologous locus in the genome of animal models because of sequence divergence, thus hampering attempts to assess the in vivo efficacy and safety of any engineered enzyme prior to its application in human trials. Here, we show that naturally occurring HEases can be found, that cleave desirable human targets. Some of these enzymes are also shown to cleave the homologous sequence in the genome of animal models. In addition, the distribution of off-target effects may be more predictable for native HEases. Based on our experimental observations, we present the HomeBase algorithm, database and web server that allow a high-throughput computational search and assignment of HEases for the targeting of specific loci in the human and other genomes. We validate experimentally the predicted target specificity of candidate fungal, bacterial and archaeal HEases using cell free, yeast and archaeal assays.

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/.

Development of a cross-European virtual sample repository and HIV resistance database

BACKGROUND: Several European HIV observational data bases have, over the last decade, accumulated a substantial number of resistance test results and developed large sample repositories, There is a need to link these efforts together, We here describe the development of such a novel tool that allows to bind these data bases together in a distributed fashion for which the control and data remains with the cohorts rather than classic data mergers.METHODS: As proof-of-concept we entered two basic queries into the tool: available resistance tests and available samples. We asked for patients still alive after 1998-01-01, and between 180 and 195 cm of height, and how many samples or resistance tests there would be available for these patients, The queries were uploaded with the tool to a central web server from which each participating cohort downloaded the queries with the tool and ran them against their database, The numbers gathered were then submitted back to the server and we could accumulate the number of available samples and resistance tests.RESULTS: We obtained the following results from the cohorts on available samples/resistance test: EuResist: not availableI11,194; EuroSIDA: 20,71611,992; ICONA: 3,751/500; Rega: 302/302; SHCS: 53,78311,485, In total, 78,552 samples and 15,473 resistance tests were available amongst these five cohorts. Once these data items have been identified, it is trivial to generate lists of relevant samples that would be usefuI for ultra deep sequencing in addition to the already available resistance tests, Saon the tool will include small analysis packages that allow each cohort to pull a report on their cohort profile and also survey emerging resistance trends in their own cohort,CONCLUSIONS: We plan on providing this tool to all cohorts within the Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN) and will provide the tool free of charge to others for any non-commercial use, The potential of this tool is to ease collaborations, that is, in projects requiring data to speed up identification of novel resistance mutations by increasing the number of observations across multiple cohorts instead of awaiting single cohorts or studies to reach the critical number needed to address such issues.

WWW-sivuston kävijäseurannan uudistaminen

Julkisista WWW-sivustoista on tullut yrityksille tärkeitä markkinointikanavia ja niiden kehittämiseen ja ylläpitoon panostetaan yhä enemmän. Yritykset tarvitsevat kuitenkin myös mahdollisuuden mitata sivuston tavoitteiden onnistumista. Tähän tarkoitukseen on kehitetty erilaisia kävijäseurantaohjelmistoja, jotka raportoivat sivuston kävijäliikenteen määriä ja asetettujen tavoitteiden toteutumista. Tässä työssä käsitellään WWW-sivustojen kävijäseurannan mahdollisuuksia ja erilaisia seurantaan soveltuvia menetelmiä.Suosituimpia menetelmiä ovat WWW-palvelimen lokitiedostojen analysointi, evästeet ja sivuihin upotettavat jäljitteet. Työssä mietittiin myös yksityisyyden suojaa, joka tulee ottaa huomioon, kun kävijöistä aletaan kerätä tietoa. Työn tarkoituksena oli löytää Vaisalan sivustoille sopiva kävijäseurantamenetelmä ja uusi ohjelmisto, joka toteuttaa tarvittavat vaatimukset. Mahdollisia kävijäseurantaohjelmistoja testattiin Vaisalan julkisella WWW-sivustolla ja testaustulosten perusteella otettiin käyttöön jäljitteillä toimiva kävijäseurantaohjelmisto. Ohjelmiston avulla saadaan huomattavasti aikaisempaa tarkempaa tietoa WWW-sivujen käytöstä. Uusi tieto helpottaa sivuston kehitystyötä ja sitä käytetään myös markkinoinnin ja erilaisten tulosmittarien tarpeisiin.

Gestió de la informació d'interès d'un treballador autònom

L’objectiu principal d’aquest treball és fer un programa que permeti portar la informació que un treballador autònom li interessa, d’acord amb les seves necessitats. En el nostre cas es tracta d’un centre d’estètica, que té més d’una seu, el qual li interessa portar tota la cartilla de clients, centres associats, proveïdors ... a més de poder fer les factures corresponents als centres associats, poder calcular en el moment que en el treballador li interessi, els ingressos realitzats durant un període de temps determinat i poder portar una agenda actualitzada dels dos centres, on es mostren totes les visites que hi ha en un dia. Per tal de realitzar el programa, s’han portat a terme mitjançant dos aplicacions, i connectant-los en una base de dades. Per una banda tenim una aplicació implementada amb C++, per l’altra, una pàgina web amb PHP, finalment com a sistema gestor de base de dades utilitzem el MySQL Server. El programa fet amb C++, consta de tota la part d’entrada i/o modificacions de dades, en aquesta part només hi pot accedir el treballador autònom, ja que és la única persona que pot fer aquesta feina. En la pàgina web, hi pot accedir qualsevol persona que tingui un nom d’usuari i una contrasenya. A través de la web es pot fer qualsevol tipus de consulta, fer tot el control de les agendes, portar a terme tot el tema de facturació i ingressos, i com a excepció l’entrada de dades de clients, ja que s’ha de poder realitzar en qualsevol moment i lloc. Per acabar, tenim la necessitat de tenir un servidor, aquest ha d’estar format, mínim, per la base de dades. Com que l’aplicació amb C++ i la base de dades han d’estar ubicades al mateix lloc. A més, necessitem un servidor web per tal de tenir la nostra pàgina a la xarxa, per aconseguir això, utilitzem un programa anomenat DynDNS, que es fa servir per a convertir una IP dinàmica en una IP estàtica i d’aquesta manera convertir un ordinador qualsevol amb un servidor web.

Mobiilin työajanhallinnan ohjelmistokehitys

Työajan seuranta ja kohdistaminen oikeisiin kustannuslajeihin on yrityksen suorituskyvyn ja kasvun kannalta usein välttämättömyys. Tässä työssä tutkitaan mobiiliteknologioiden mahdollisuuksia ja soveltuvuutta tuottaa palveluita työajan hallinnointiin, valitaan sopiva arkkitehtuuri ja kehitetään Java ME –teknologialla prototyyppi, joka on helposti integroitavissa yrityksen nykyisiin palvelinpuolen järjestelmiin ja tietokantoihin. Työn sovellusosuudessa kuvataan prototyypin ohjelmoinnissa käytetyt työkalut, menetelmät, ongelmakohdat sekä niiden ratkaisut. Suunnitelluissa käyttötapauksissa tapahtumatiedot syötetään manuaalisesti puhelimen käyttöliittymän kautta tai automatisoidummin kerätään kustannuskohdistetietoa työkohteisiin sijoitetuista NFC-tageista. Työaikaleimaamista testattiin emulaattorilla ja oikealla matkapuhelimella. Lopputuloksena asiakkaan työajanhallinnan tapahtumat siirtyvät langattomasti ja reaaliaikaisesti yrityksen webpalvelimelle JSON-formaatissa.

The GATO gene annotation tool for research laboratories

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.