Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)

Abstract Background An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of the same class, and not only variability due to technical sampling error. Results We introduce a Bayesian model that accounts for the within-class variability by means of mixture distribution. We show that the previously available approaches of aggregation in pools ("pseudo-libraries") and the Beta-Binomial model, are particular cases of the mixture model. We illustrate our method with a brain tumor vs. normal comparison using SAGE data from public databases. We show examples of tags regarded as differentially expressed with high significance if the within-class variability is ignored, but clearly not so significant if one accounts for it. Conclusion Using available information about biological replicates, one can transform a list of candidate transcripts showing differential expression to a more reliable one. Our method is freely available, under GPL/GNU copyleft, through a user friendly web-based on-line tool or as R language scripts at supplemental web-site.

Web 2.0, contenuti aperti e produzione tra pari: analisi economica delle possibili sinergie.

Analisi in chiave economica e sociale dell'evoluzione di Internet, delle tecnologie legate al Web 2.0, dei fenomeni della pirateria, del software libero ed open source, del copyleft, dei contenuti aperti e della produzione tra pari. Introduzione dei concetti di economia del gratis ("freeconomics") e di coda lunga. Consigli manageriali pratici per i nuovi mercati digitali e per la competizione nella rete Internet.

Open Source und Kartellrecht

„Open source and European antitrust laws: An analysis of copyleft and the prohibition of software license fees on the basis of art. 101 TFEU and the block exemptions“ Open source software and open source licenses (like the GNU GPL) are not only relevant for computer nerds or activists – they are already business. They are for example the fundament of LINUX, the only real rival of MICROSOFT’s WINDOWS-line in the field of operating systems for IBM PC compatibles. Art. 101 TFEU (like the identical predecessor art. 81 TEC) as part of the EU antitrust laws prohibits contract terms like price fixing and some forms of technology control. Are copyleft – the „viral effect“, the „cancer“ – and the interdiction of software license fees in the cross hairs of this legal rule? On the other side the European Union has since 2004 a new Technology Transfer Block Exemption with software license agreements for the first time in its scope: a safe harbour and a dry place under a umbrella for open source software? After the introduction (A) with a description of open source software the following text analyses the system of the European Unions competition law respectivley antitrust law and the requirements of the block exemptions (B). Starting point of antitrust analysis are undertakings – but who are the untertakings (C) in the field of widespread, independent developers as part of the „bazar organization“? To see how much open source has to fear from the law of the European Union, at the end the anti competitive and pro competitive effects of open source are totalized within the legal framework (D). The conclusion (E) shows: not nothing, but not much.

Listen to the mocking bird : satiric songs to tunes you know /

On verso of t.p.: "Copyleft 1971, 1972, 1973."

Attaching unit costs to Australia's National Survey of Mental Health and Wellbeing

Background: In mental health, policy-makers and planners are increasingly being asked to set priorities. This means that health economists, health services researchers and clinical investigators are being called upon to work together to define and measure costs. Typically, these researchers take available service utilisation data and convert them to costs, using a range of assumptions. There are inefficiencies, as individual groups of researchers frequently repeat essentially similar exercises in achieving this end. There are clearly areas where shared or common investment in the development of statistical software syntax, analytical frameworks and other resources could maximise the use of data. Aims of the Study: This paper reports on an Australian project in which we calculated unit costs for mental health admissions and community encounters. In reporting on these calculations, our purpose is to make the data and the resources associated with them publicly available to researchers interested in conducting economic analyses, and allow them to copy, distribute and modify them, providing that all copies and modifications are available under the same terms and conditions (i.e., in accordance with the 'Copyleft' principle), Within this context, the objectives of the paper are to: (i) introduce the 'Copyleft' principle; (ii) provide an overview of the methodology we employed to derive the unit costs; (iii) present the unit costs themselves; and (iv) examine the total and mean costs for a range of single and comorbid conditions, as an example of the kind of question that the unit cost data can be used to address. Method: We took relevant data from the Australian National Survey of Mental Health and Wellbeing (NSMHWB), and developed a set of unit costs for inpatient and community encounters. We then examined total and mean costs for a range of single and comorbid conditions. Results: We present the unit costs for mental health admissions and mental health community contacts. Our example, which explored the association between comorbidity and total and mean costs, suggested that comorbidly occurring conditions cost more than conditions which occur on their own. Discussion: Our unit costs, and the materials associated with them, have been published in a freely available form governed by a provision termed 'Copyleft'. They provide a valuable resource for researchers wanting to explore economic questions in mental health. Implications for Health Policies: Our unit costs provide an important resource to inform economic debate in mental health in Australia, particularly in the area of priority-setting. In the past, such debate has largely, been based on opinion. Our unit costs provide the underpinning to strengthen the evidence-base of this debate. Implications for Further Research: We would encourage other Australian researchers to make use of our unit costs in order to foster comparability across studies. We would also encourage Australian and international researchers to adopt the 'Copyleft' principle in equivalent circumstances. Furthermore, we suggest that the provision of 'Copyleft'-contingent funding to support the development of enabling resources for researchers should be considered in the planning of future large-scale collaborative survey work, both in Australia and overseas.