DnaSP v5: A software for comprehensive analysis of DNA polymorphism data

DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.

Lawyer-info : Software de atención al cliente para despachos de abogados en dispositivos móviles Android

Este trabajo desarrolla una aplicación basada en la tecnología Android para la atención de clientes en despachos de abogados.

Cooperación y teoría de juegos, el software libre o el #15m, dos ejemplos para la universidad

Xerrada de cloenda de la Setmana internacional d'accés obert 2011 a la UOC, a càrrec de l'advocat Josep Jover. Per què les estratègies altruistes guanyen les egoistes en el programari lliure i en el #15m? El moviment #15m, igual que el programari, a diferència dels béns materials, no es pot posseir, ja que en pot gaudir (formant-ne part) un nombre indeterminat de persones sense que per això hagi de privar ningú de tenir-lo al seu torn. I això porta a girar com un mitjó la manera com manegen la informació les universitats, i quina és la missió de la universitat en la nova societat. En el futur immediat, valorarem les universitats no per la informació que guarden, que fora sempre serà millor i més extensa, sinó per la capacitat de crear masses crítiques, sia de recerca de coneixement, de capacitació humana, d'enllaç entre iguals... Les universitats hauran d'implantar el model o quedaran relegades.

Cooperation and game theory, free software or the #15m movement: Two examples for universities

Closing talk of the Open Access Week 2011 at the UOC, by Josep Jover. Why do altruistic strategies beat selfish ones in the spheres of both free software and the #15m movement? The #15m movement, like software but unlike tangible goods, cannot be owned. It can be used (by joining it) by an indeterminate number of people without depriving anyone else of the chance to do the same. And that turns everything on its head: how universities manage information and what their mission is in this new society. In the immediate future, universities will be valued not for the information they harbour, which will always be richer and more extensive beyond their walls, but rather for their capacity to create critical masses, whether of knowledge research, skill-building, or networks of peers... universities must implement the new model or risk becoming obsolete.

Monitoring of noninvasive ventilation by built-in software of home bilevel ventilators: a bench study.

BACKGROUND: Current bilevel positive-pressure ventilators for home noninvasive ventilation (NIV) provide physicians with software that records items important for patient monitoring, such as compliance, tidal volume (Vt), and leaks. However, to our knowledge, the validity of this information has not yet been independently assessed. METHODS: Testing was done for seven home ventilators on a bench model adapted to simulate NIV and generate unintentional leaks (ie, other than of the mask exhalation valve). Five levels of leaks were simulated using a computer-driven solenoid valve (0-60 L/min) at different levels of inspiratory pressure (15 and 25 cm H(2)O) and at a fixed expiratory pressure (5 cm H(2)O), for a total of 10 conditions. Bench data were compared with results retrieved from ventilator software for leaks and Vt. RESULTS: For assessing leaks, three of the devices tested were highly reliable, with a small bias (0.3-0.9 L/min), narrow limits of agreement (LA), and high correlations (R(2), 0.993-0.997) when comparing ventilator software and bench results; conversely, for four ventilators, bias ranged from -6.0 L/min to -25.9 L/min, exceeding -10 L/min for two devices, with wide LA and lower correlations (R(2), 0.70-0.98). Bias for leaks increased markedly with the importance of leaks in three devices. Vt was underestimated by all devices, and bias (range, 66-236 mL) increased with higher insufflation pressures. Only two devices had a bias < 100 mL, with all testing conditions considered. CONCLUSIONS: Physicians monitoring patients who use home ventilation must be aware of differences in the estimation of leaks and Vt by ventilator software. Also, leaks are reported in different ways according to the device used.

Legal Issues for FOSS-based Supply Chain Management ¿ Black Duck Software

Open source is typically outside of normal commercial software procurement processes.The Challenges.Increasingly diverse and distributed set of development resources.Little/no visibility into the origins of the software.Supply Chain Comparison: Hardware vs Software.Open source has revolutionized the mobile and device landscape, other industries will follow.Supply chain management techniques from hardware are useful for managing software.SPDX A standard format for communicating a software Bill of Materials across the supply chain.Effective management and control requires training, tools, processes and standards.

Open Source Software : the Intersection of IP and Security in Open Source

The use of open source software continues to grow on a daily basis. Today, enterprise applications contain 40% to 70% open source code and this fact has legal, development, IT security, risk management and compliance organizations focusing their attention on its use, as never before. They increasingly understand that the open source content within an application must be detected. Once uncovered, decisions regarding compliance with intellectual property licensing obligations must be made and known security vulnerabilities must be remediated. It is no longer sufficient from a risk perspective to not address both open source issues.

Contracting with free software communities

Industry and large Agencies needs ¿agile¿ programming resources, to reinforce their own development staff and take advantage of innovative approaches produced by ¿fresh minds¿ all over the world. At the same time they may be reluctant to engage in classical software development call for tenders and contracts. Such contracts are often ¿trusted¿ by large ICT firms, which will deliver according to their own rigid frameworks (often based on alliances with proprietary software vendors), may propose comfortable quality assurances, but will cover their (real) risks and liability with high contingency costs and will charge for any change request in case the original specifications have not fixed all possible issues. Introducing FLOSS in business implies a new contracting philosophy, based on incentives rather than penalties and liability. Based on 2011 experience with a large Space Agency, Patrice-Emmanuel Schmitz pictures the needed legal instruments for a novel approach.

Free Open Source Software and Dual-Use: Loophole or Dissent?

The Free Open Source Software (FOSS) seem far from the military field but in some cases, some technologies normally used for civilian purposes may have military applications. These products and technologies are called dual-use. Can we manage to combine FOSS and dual-use products? On one hand, we have to admit that this kind of association exists - dual-use software can be FOSS and many examples demonstrate this duality - but on the other hand, dual-use software available under free licenses lead us to ask many questions. For example, the dual-use export control laws aimed at stemming the proliferation of weapons of mass destruction. Dual-use export in United States (ITAR) and Europe (regulation 428/2009) implies as a consequence the prohibition or regulation of software exportation, involving the closing of source code. Therefore, the issues of exported softwares released under free licenses arises. If software are dual-use goods and serve for military purposes, they may represent a danger. By the rights granted to licenses to run, study, redistribute and distribute modified versions of the software, anyone can access the free dual-use software. So, the licenses themselves are not at the origin of the risk, it is actually linked to the facilitated access to source codes. Seen from this point of view, it goes against the dual-use regulation which allows states to control these technologies exportation. For this analysis, we will discuss about various legal questions and draft answers from either licenses or public policies in this respect.

Smart antennas in software radio base stations

The application of adaptive antenna techniques to fixed-architecture base stations has been shown to offer wide-ranging benefits, including interference rejection capabilities or increased coverage and spectral efficiency.Unfortunately, the actual implementation ofthese techniques to mobile communication scenarios has traditionally been set back by two fundamental reasons. On one hand, the lack of flexibility of current transceiver architectures does not allow for the introduction of advanced add-on functionalities. On the other hand, theoften oversimplified models for the spatiotemporal characteristics of the radio communications channel generally give rise toperformance predictions that are, in practice, too optimistic. The advent of software radio architectures represents a big step toward theintroduction of advanced receive/transmitcapabilities. Thanks to their inherent flexibilityand robustness, software radio architecturesare the appropriate enabling technology for theimplementation of array processing techniques.Moreover, given the exponential progression ofcommunication standards in coexistence andtheir constant evolution, software reconfigurabilitywill probably soon become the only costefficientalternative for the transceiverupgrade. This article analyzes the requirementsfor the introduction of software radio techniquesand array processing architectures inmultistandard scenarios. It basically summarizesthe conclusions and results obtained withinthe ACTS project SUNBEAM,1 proposingalgorithms and analyzing the feasibility ofimplementation of innovative and softwarereconfigurablearray processing architectures inmultistandard settings.

Software Process Modeling with Eclipse Process Framework

The software development industry is constantly evolving. The rise of the agile methodologies in the late 1990s, and new development tools and technologies require growing attention for everybody working within this industry. The organizations have, however, had a mixture of various processes and different process languages since a standard software development process language has not been available. A promising process meta-model called Software & Systems Process Engineering Meta- Model (SPEM) 2.0 has been released recently. This is applied by tools such as Eclipse Process Framework Composer, which is designed for implementing and maintaining processes and method content. Its aim is to support a broad variety of project types and development styles. This thesis presents the concepts of software processes, models, traditional and agile approaches, method engineering, and software process improvement. Some of the most well-known methodologies (RUP, OpenUP, OpenMethod, XP and Scrum) are also introduced with a comparison provided between them. The main focus is on the Eclipse Process Framework and SPEM 2.0, their capabilities, usage and modeling. As a proof of concept, I present a case study of modeling OpenMethod with EPF Composer and SPEM 2.0. The results show that the new meta-model and tool have made it possible to easily manage method content, publish versions with customized content, and connect project tools (such as MS Project) with the process content. The software process modeling also acts as a process improvement activity.

Manipulació geomètrica dels blocs d'AutoCAD

Aquest text és un recull de procediments per inserir els blocs d'AutoCAD de forma més eficient, en la resolució de problemes prèviament tipificats: la PRIMERA PART descriu protocols d'actuació que l'usuari haurà d'aplicar manualment, mentre que la SEGONA PART ofereix rutines programades en AutoLISP i VisualLISP que l'eximiran d'aquesta obligació.Si ho deixéssim aquí, però, podria semblar que els mateixos mètodes manuals presentats en primer lloc són després els que AutoLISP automatitza; per això convé aclarir que la problemàtica de la PRIMERA PART, tot i que pròxima a la de la SEGONA, és diferent i reprodueix el contingut d'una monografia (BLOCS I GEOMETRIA: 5 EXERCICIS COMENTATS) que forma part del material de suport a l'assignatura ELEMENTS DE CAD, impartida per l'autor en l'ETS d'Enginyeria de Telecomunicació de Barcelona i que té per objecte cobrir el buit bibliogràfic que es detectava en el vessant geomètric de la inserció de blocs, a diferència del que s'ocupa de l'estructura de dades més adient en cada context (incrustació de dibuixos amb INSERT versus vinculació mitjançant REFX), més profusament tractat, proposant una sistematització tipològica dels casos on l'escala és funció lineal d'una distància.La SEGONA PART va més enllà i amplia el repertori d'AutoCAD amb les ordres GINSERT, RATREDIT, INSERTOK, INS2D, INS3D, BLOQUEOK, DESCOMPOK, DEF-TRANSF, APL-TRANSF-V i APL-TRANSF-N, de les quals INS2D i INS3D (INSERTOK és una versió simplificada de INS2D, per a blocs sense atributs) són l'aportació més innovadora i que més lluny porta les potencialitats de la inserció de blocs: resumint-ho en una frase, es tracta d’aconseguir que la inserció d’un bloc (que pot ser l’original, un bloc constituït per una inserció de l’original o un de constituït per la inserció del precedent) s’encabeixi en un marc prèviament establert, a semblança de les ordres ESCALA o GIRA, que mitjançant l'opció Referencia apliquen als objectes seleccionats la transformació d'escalat o de rotació necessària per tal que un element de referència assoleixi una determinada grandària o posició. Tot i que, per identificar amb encert el nucli del problema, serà inevitable introduir una reflexió: quan s’ha tingut la precaució de referir un bloc 2D a un quadrat unitari ortogonal, inserir-lo de manera que s’adapti a qualsevol marc rectangular establert en el dibuix és immediat, però ja no ho és tant concatenar insercions de manera que, a més d’una combinació simple de escalat, gir i translació, l’operació dugui implícita una transformació de cisallament. Perquè és clar que si inserim el bloc girat i convertim la inserció en un bloc que al seu torn tornem a inserir, ara però amb escalat no uniforme, el transformat del quadrat de referència primitiu serà un paral·lelogram, però el problema és: dibuixat un marc romboïdal concret, ¿quin gir caldrà donar a la primera inserció, i quin gir i factors d’escala caldrà aplicar a la segona perquè el quadrat de referència s’adapti al marc? El problema es complica si, a més, volem aprofitar el resultat de la primera inserció per a d’altres paral·lelograms, organitzant un sistema no redundant de insercions intermèdies. Doncs bé: INS2D i INS3D donen satisfacció a aquestes qüestions (la segona ja no contempla l'encaix en un paral·lelogram, sinó en un paral·lelepípede) i són aplicables a blocs proveïts d’atributs, no només de tipus convencional (els continguts en el pla de base del bloc, únics de funcionament garantit amb l’ordre INSERT), sinó també dels situats i orientats lliurement.