6478208
Chemistry in Bioinformatics
AbstractChemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.
1936302
Communication and re-use of chemical information in bioscience
The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.
16397953
Parametricity and Variants of Girard's J Operator
Abstract The Girard–Reynolds polymorphic λ -calculus is generally regarded as a calculus of parametric polymorphism in which all well-formed terms are strongly normalizing with respect to β -reductions. Girard demonstrated that the addition of a simple “non-parametric” operation, J , to the calculus allows the definition of a non-normalizing term. Since the type of J is not inhabited by any closed term, one might suspect that this may play a role in defining a non-normalizing term using it. We demonstrate that this is not the case by giving a simple variant, J′ , of J whose type is otherwise inhabited and which causes normalization to fail. It appears that impredictivity is essential to the argument; predictive variants of the polymorphic λ -calculus admit non-parametric operations without sacrificing normalization.
8879002
Status of clinical gene sequencing data reporting and associated risks for information loss
Clinical gene sequencing is growing in importance and cost-effectiveness. In the past two years, the number of genes associated with disease has grown by roughly 25%. Knowledge of genetic variations will soon guide drug selection and dosages, predict risks from toxin exposures, and inform nutritional needs. Despite the significance of sequencing, methods for reporting results are problematic. Frequent use of paper and infrequent use of naming standards impede data exchange and make incorporation into the electronic medical record difficult. Reports often describe only variations found, rather than all data (all patient bases sequenced). Also, reports frequently do not describe reference data used to define variations. These practices create risks for loss of both data and information. Standardized electronic reporting of all data (all bases sequenced and all reference data) and electronic record systems capable of storing these results would both prevent data loss and simplify the preservation of information those data provide.
2138308
Contract Signing, Optimism, and Advantage
A contract signing protocol lets two parties exchange digital signatures on a pre-agreed text. Optimistic contract signing protocols enable the signers to do so without invoking a trusted third party. However, an adjudicating third party remains available should one or both signers seek timely resolution. We analyze optimistic contract signing protocols using a game-theoretic approach and prove a fundamental impossibility result: in any fair, optimistic, timely protocol, an optimistic player yields an advantage to the opponent. The proof relies on a careful characterization of optimistic play that postpones communication to the third party. Since advantage cannot be completely eliminated from optimistic protocols, we argue that the strongest property attainable is the absence of provable advantage, i.e., abuse-freeness in the sense of Garay-Jakobsson-MacKenzie.
42803318
File Servers
This chapter discusses file servers that are accessible via some form of local network or internetwork. It characterizes file services from the client point of view along a number of dimensions; distributivity of the service itself, the network environment of the service, the file model supported by the service, the kind(s) of atomic update provided by the service, the techniques used for controlling the allocation of files. It then describes the client interfaces to three existing file services. Finally, the impact of these features on design and implementation is discussed. An appendix contains characterizations of a variety of existing network-based file services using the criteria developed in the chapter.
1053621
Privacy and contextual integrity: framework and applications
Contextual integrity is a conceptual framework for understanding privacy expectations and their implications developed in the literature on law, public policy, and political philosophy. We formalize some aspects of contextual integrity in a logical framework for expressing and reasoning about norms of transmission of personal information. In comparison with access control and privacy policy frameworks such as RBAC, EPAL, and P3P, these norms focus on who personal information is about, how it is transmitted, and past and future actions by both the subject and the users of the information. Norms can be positive or negative depending on whether they refer to actions that are allowed or disallowed. Our model is expressive enough to capture naturally many notions of privacy found in legislation, including those found in HIPAA, COPPA, and GLBA. A number of important problems regarding compliance with privacy norms, future requirements associated with specific actions, and relations between policies and legal standards reduce to standard decision procedures for temporal logic