Compositions in life science data

The aim of this talk is to convince the reader that there are a lot of interesting statisticalproblems in presentday life science data analysis which seem ultimately connected withcompositional statistics.Key words: SAGE, cDNA microarrays, (1D-)NMR, virus quasispecies

How Much Does It Cost? Optimization of Costs in Sequence Analysis of Social Science Data

One major methodological problem in analysis of sequence data is the determination of costs from which distances between sequences are derived. Although this problem is currently not optimally dealt with in the social sciences, it has some similarity with problems that have been solved in bioinformatics for three decades. In this article, the authors propose an optimization of substitution and deletion/insertion costs based on computational methods. The authors provide an empirical way of determining costs for cases, frequent in the social sciences, in which theory does not clearly promote one cost scheme over another. Using three distinct data sets, the authors tested the distances and cluster solutions produced by the new cost scheme in comparison with solutions based on cost schemes associated with other research strategies. The proposed method performs well compared with other cost-setting strategies, while it alleviates the justification problem of cost schemes.

Implementing statistical learning methods through Bayesian networks. Part 1: a guide to Bayesian parameter estimation using forensic science data

As a thorough aggregation of probability and graph theory, Bayesian networks currently enjoy widespread interest as a means for studying factors that affect the coherent evaluation of scientific evidence in forensic science. Paper I of this series of papers intends to contribute to the discussion of Bayesian networks as a framework that is helpful for both illustrating and implementing statistical procedures that are commonly employed for the study of uncertainties (e.g. the estimation of unknown quantities). While the respective statistical procedures are widely described in literature, the primary aim of this paper is to offer an essentially non-technical introduction on how interested readers may use these analytical approaches - with the help of Bayesian networks - for processing their own forensic science data. Attention is mainly drawn to the structure and underlying rationale of a series of basic and context-independent network fragments that users may incorporate as building blocs while constructing larger inference models. As an example of how this may be done, the proposed concepts will be used in a second paper (Part II) for specifying graphical probability networks whose purpose is to assist forensic scientists in the evaluation of scientific evidence encountered in the context of forensic document examination (i.e. results of the analysis of black toners present on printed or copied documents).

PROM-OPEN: PROMOTING OPEN SCIENCE IN AN ON-LINE E-LEARNING ENVIRONMENT

Peer-reviewed

Legal challenges for next generation science

Presentation at the Nordic Perspectives on Open Access and Open Science seminar, Helsinki, October 15, 2013

Open research data policies, what makes the difference?

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Recent developments in Finland – Open Science, IT infrastructures

Presentation of Kristiina Hormia-Poutanen at the LIBER Board meeting, February 19, 2015 in Helsinki.

Compositions in life science data

The aim of this talk is to convince the reader that there are a lot of interesting statistical problems in presentday life science data analysis which seem ultimately connected with compositional statistics. Key words: SAGE, cDNA microarrays, (1D-)NMR, virus quasispecies

Open Equipment data flow

Short set of slides explaining the workflow from a university website to equipment.data.ac.uk

Extracting Causal Graphs from an Open Provenance Data Model

The open provenance architecture (OPA) approach to the challenge was distinct in several regards. In particular, it is based on an open, well-defined data model and architecture, allowing different components of the challenge workflow to independently record documentation, and for the workflow to be executed in any environment. Another noticeable feature is that we distinguish between the data recorded about what has occurred, emphprocess documentation, and the emphprovenance of a data item, which is all that caused the data item to be as it is and is obtained as the result of a query over process documentation. This distinction allows us to tailor the system to separately best address the requirements of recording and querying documentation. Other notable features include the explicit recording of causal relationships between both events and data items, an interaction-based world model, intensional definition of data items in queries rather than relying on explicit naming mechanisms, and emphstyling of documentation to support non-functional application requirements such as reducing storage costs or ensuring privacy of data. In this paper we describe how each of these features aid us in answering the challenge provenance queries.

Data cloud through google cloud storage

Il Cloud Storage è un modello di conservazione dati su computer in rete, dove i dati stessi sono memorizzati su molteplici server, reali e/o virtuali, generalmente ospitati presso strutture di terze parti o su server dedicati. Tramite questo modello è possibile accedere alle informazioni personali o aziendali, siano essi video, fotografie, musica, database o file in maniera “smaterializzata”, senza conoscere l’ubicazione fisica dei dati, da qualsiasi parte del mondo, con un qualsiasi dispositivo adeguato. I vantaggi di questa metodologia sono molteplici: infinita capacita’ di spazio di memoria, pagamento solo dell’effettiva quantità di memoria utilizzata, file accessibili da qualunque parte del mondo, manutenzione estremamente ridotta e maggiore sicurezza in quanto i file sono protetti da furto, fuoco o danni che potrebbero avvenire su computer locali. Google Cloud Storage cade in questa categoria: è un servizio per sviluppatori fornito da Google che permette di salvare e manipolare dati direttamente sull’infrastruttura di Google. In maggior dettaglio, Google Cloud Storage fornisce un’interfaccia di programmazione che fa uso di semplici richieste HTTP per eseguire operazioni sulla propria infrastruttura. Esempi di operazioni ammissibili sono: upload di un file, download di un file, eliminazione di un file, ottenere la lista dei file oppure la dimensione di un dato file. Ogniuna di queste richieste HTTP incapsula l’informazione sul metodo utilizzato (il tipo di richista, come GET, PUT, ...) e un’informazione di “portata” (la risorsa su cui effettuare la richiesta). Ne segue che diventa possibile la creazione di un’applicazione che, facendo uso di queste richieste HTTP, fornisce un servizio di Cloud Storage (in cui le applicazioni salvano dati in remoto generalmene attraverso dei server di terze parti). In questa tesi, dopo aver analizzato tutti i dettagli del servizio Google Cloud Storage, è stata implementata un’applicazione, chiamata iHD, che fa uso di quest’ultimo servizio per salvare, manipolare e condividere dati in remoto (nel “cloud”). Operazioni comuni di questa applicazione permettono di condividere cartelle tra più utenti iscritti al servizio, eseguire operazioni di upload e download di file, eliminare cartelle o file ed infine creare cartelle. L’esigenza di un’appliazione di questo tipo è nata da un forte incremento, sul merato della telefonia mobile, di dispositivi con tecnologie e con funzioni sempre più legate ad Internet ed alla connettività che esso offre. La tesi presenta anche una descrizione delle fasi di progettazione e implementazione riguardanti l’applicazione iHD. Nella fase di progettazione si sono analizzati tutti i requisiti funzionali e non funzionali dell’applicazione ed infine tutti i moduli da cui è composta quest’ultima. Infine, per quanto riguarda la fase di implementazione, la tesi presenta tutte le classi ed i rispettivi metodi presenti per ogni modulo, ed in alcuni casi anche come queste classi sono state effettivamente implementate nel linguaggio di programmazione utilizzato.