Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Information Outlook, May 2004

Volume 8, Issue 5https://scholarworks.sjsu.edu/sla_io_2004/1004/thumbnail.jp

The English pronunciation teaching in Europe survey: selected results

The results of EPTiES reveal interesting phenomena across Europe, despite shortcomings in terms of construction and distribution. For example, most respondents are non-native speakers of English and the majority of them rate their own mastery of English pronunciation favourably. However, most feel they had little or no training in how to teach pronunciation, which begs the question of how teachers are coping with this key aspect of language teaching. In relation to target models, RP remains the variety of English which teachers claim to use, whilst recognizing that General American might be preferred by some students. Differences between countries are explored, especially via replies to open-ended questions, allowing a more nuanced picture to emerge for each country. Other survey research is also referred to, in order to contextualise the analyses and implications for teaching English and for training English teacher

Simulation of networks of spiking neurons: A review of tools and strategies

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of Computational Neuroscience, in press (2007

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

U.S.-EU Safe Harbor Framework; A Guide to Self-Certification

[Excerpt] In this guide, we have provided an outline of the most critical pieces of the Safe Harbor Framework. The application is made available, along with a Helpful Hints Guide that explains how to fill it out. The Safe Harbor Principles and FAQs are also provided for easy reference. There is also an explanation and listing of third party dispute resolution providers (or Independent Resource Mechanisms) with descriptions of the services provided by three dispute resolution providers that work with Safe Harbor. Finally, we’ve also included several sample company privacy policies for reference, and a glossary that explains key terms. We’ve broken this Guide into nine major sections, each to address different questions you might have. What follows is a brief description of each section: Overview: The overview gives some background on the Safe Harbor Framework, how it came about, and explains many of the certification requirements. The overview also lists the principles of the Safe Harbor program. Application: The Application is provided for easy reference. Applicants should apply online at http://export.gov /safeharbor (click on “Certification Form” in the right sidebar). Certification Mark: The Commerce Department’s International Trade Administration has recently developed a certification mark for the Safe Harbor Framework. The mark may be used by companies on their websites to signify that they have self-certified compliance with the provisions of the Safe Harbor Framework. Instructions for use of the certification mark are provided. Helpful Hints Guide (to Certification): The Helpful Hints Guide is meant to give quick answers to any questions a U.S. company might have about the certification process. It should be used in conjunction with the rest of the Guide, however it answers many of the most common questions about the certification process. Safe Harbor Principles: We have provided the full text of the official declaration of the Safe Harbor Principles as announced on July 21, 2000. This text is helpful for understanding the foundation of the Safe Harbor Principles and the Framework. Frequently Asked Questions: We have provided the Frequently Asked Questions in full text because they answer many of the most commonly asked questions about the Safe Harbor Framework. Dispute Resolution Providers: Here we have provided a short description of the role of dispute resolution providers (also referred to as Independent Recourse Mechanisms) and descriptions of the services they offer. Sample Privacy Policies: Here we have provided three sample privacy policies for reference, which may serve as guidance when creating a new Privacy Policy or updating an existing Privacy Policy to align it with the Safe Harbor Framework. The Safe Harbor Framework requires an affirmative commitment in the Privacy Policy to the principles of the Safe Harbor Framework. Glossary: A short glossary is also provided for many of the technical terms frequently used in the Guide

Perception of millennials toward humanitarian organisations: how millennials perceive international humanitarian organisations, their marketing methods and how does it impact their donations?

Enterprises put special attention into communication and marketing. These two aspects are continuously evolving, transforming and adapting to better reach the expectations of a potential buyer. Especially for humanitarian organisations, there is no item to sell but the customer, in this instance: the donor needs to be understood in order to, again, not make a purchase but donate money. On the one hand, the customer is buying something, and on the other, he is giving. At the end of the day an enterprise and an organisation have the same goal, they both need funds to survive. This research aims to understand the perception of Millennials towards humanitarian organisations and to address potential solutions for the pain points mentioned throughout the paper. Qualitative data have been gathered by interviews with the organisations: International Committee of the Red Cross, Médecins Sans Frontières and Terre des Hommes. This method enables the reader to gasp example of the current situation regarding the different communication mediums used such as mailings to households, billboards, celebrity endorsement so and so forth to reach the different segment of the population. It also helped understanding how organisations cope with communication guidelines when regards to choosing a picture or a content for an advertisement. Several concepts have been mentioned like “death kilometer” and “information hierarchy” which are used in communication and can impact how the information is received by the recipient. Challenges were also mentioned such as the situation of the humanitarian market, new laws affecting not only marketing departments, but also entire organisations. Quantitative data have been collected through a survey. The focus was made on Millennials living in the French part of Switzerland. 115 answers have been analysed and enable the reader to draw a picture of the situation vis-à-vis of Millennials. As results, at the exception of the 3 organisations interviewed, Millennials is split into two groups. The first one with 41% of the responses, people who already donated to an organisation, this group is then divided into occupations such as student, employees and unemployed people. The other 59%, the people who never donated to an organisation, were also divided by occupation, but the most interesting aspect is the reasons why they never donated. These latter were due to lack of financial means with the most answers, followed by mistrust toward organisations

Current Practice of Assessing and Monitoring Muscle Strength, Muscle Mass and Muscle Function during Nutritional Care by Dietitians in Switzerland—An Online Survey

Muscle parameters are recommended as diagnostic criteria for malnutrition and sarcopenia in various guidelines. However, little is known about the application of muscle parameters in daily practice of nutritional care. The aim of this study was to investigate the current practice of the application of muscle parameters, along with its promoting factors and barriers by dietitians in Switzerland. A 29-item literature-based online survey was developed and distributed via the Swiss professional association of dietitians. The data were analyzed descriptively, and relationships between demographic data and usage were examined. Dietitians (n = 117) from all three language regions completed the survey and were included in the analysis. Musculature was classified as important for the assessment of nutritional status. Body weight (89.7%), handgrip strength (87.2%), bioimpedance analysis (BIA) (87.1%) and Body Mass Index (66.7%) were considered as most significant for evaluation of nutritional status. Seventy-point nine percent (70.9%) of dietitians include at least one muscle parameter in their assessment; BIA was the parameter most often included (73.5%). However, the frequency of use of muscle parameter in daily practice was rather low. Only 23.1% applied BIA on a weekly basis. Lack of knowledge (78.6%), practical experience (71.8%) and lack of equipment (77.8%) were most frequently stated as barriers for usage. The general application of muscle parameters in nutritional care is still lacking. There is an opportunity to further strengthen diagnosis and patient monitoring via a stronger application of muscle parameters in daily practice. Practical training and education could help promote their application