Submitted to the faculty of the School of Informatics in partial fulfillment of the requirements for the degree Master of Science in Chemical Informatics (Laboratory Informatics Specialization), Indiana University, June 2006 / Industry and academic laboratories have long resisted conversion to electronic laboratory notebooks (ELN) while at the same time integrating many other kinds of information systems, most notably laboratory information management systems (LIMS), chromatography data systems (CDS), and scientific data management systems (SDMS), within laboratory operations. Scientists in both academia and industry stand to gain important functionality unavailable with paper notebooks with the adoption of ELNs such as comprehensive searching of notebooks (keyword, result, and molecular structure/substructure searching, for example); distributed availability; and long term access to data. Currently, most laboratory information systems operate independently, requiring manual data entry by users into each individual system. This process creates data and information disparities as well as creating poor referential integrity within experimental metadata. Electronic laboratory notebooks would provide a logical point around which experiment details and observations could be centered electronically. Through an ELN, experimental documentation or metadata could be communicated automatically with a LIMS, SDMS, or CDS without analyst involvement. This “electronically connected” system would allow analysts to perform their responsibilities without the interruption of independent information systems thus increasing analyst productivity and reducing user entry errors into data management systems. The thesis project consisted of two phases: the first phase was the implementation of an ELN and the second phase was the development of a software developer kit (SDK) for LABTrack based on Web Services. In the first phase of the project the adoption of an ELN, was studied within a classroom laboratory (G823 Introduction to Cell Biology) over the course of one academic semester. In the second phase of the project an SDK for LABTrack was developed to allow the importation of information from custom developed applications into LABTrack. Finally, a web portal integrating LABTrack and NuGenesis was developed to demonstrate the capabilities of the LABTrack SDK and existing capabilities of the NuGenesis SDK.

Submitted by Priscilla Araujo (priscilla@ibict.br) on 2017-08-08T19:22:05Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) anne_clinio_doutorado_final_14-06-17.pdf: 3610602 bytes, checksum: 90154e1d6df62ef68c8c3119f52f7b84 (MD5) / Made available in DSpace on 2017-08-08T19:22:05Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) anne_clinio_doutorado_final_14-06-17.pdf: 3610602 bytes, checksum: 90154e1d6df62ef68c8c3119f52f7b84 (MD5) Previous issue date: 2016-08-04 / Descrevemos e analisamos novas culturas epistêmicas (KNORR-CETINA, 1999) que estão sendo engendradas por dois modos de ciência emergentes – a Ciência Aberta e a Ciência Comum – e que, apesar de inúmeras diferenças, convergem na crítica à noção de fato científico e na estratégia de transformar o caderno de laboratório em sua principal tecnologia literária. Adotamos a noção de cultura epistêmica para operacionalizar nossa análise sobre estratégias para configuração de objetos, tecnologias e sujeitos epistêmicos por sistemas de produção de conhecimento que, por sua vez, criam efeitos de verdade. Para tal, nos inspiramos nas etnografias de laboratório e na abordagem das “três tecnologias” de Shapin e Shaffer (1985) para explicar como os filósofos naturais do século XVII construíram a noção de fato científico (matter of fact) como uma “variedade de conhecimento” tão sólida que se tornou sinônimo de ciência. De modo análogo, procuramos compreender como os modos de ciência emergentes pretendem legitimar novas maneiras de produzir conhecimento e disputar a própria noção de ciência. No movimento contemporâneo da Ciência Aberta, abordamos o open notebook science, tal como proposto em 2006 pelo professor e pesquisador em Química Jean-Claude Bradley como “uma maneira de fazer ciência na qual – da melhor maneira possível – você torna toda a sua pesquisa livre e acessível ao público em tempo real” (BRADLEY, set 2010). Adentramos seu “laboratório aberto” através de uma pesquisa documental que identificou o caderno aberto como principal elemento de um complexo ecossistema de colaboração aberta. Articulada com tecnologias sociais e materiais, esta tecnologia literária pretende substituir uma ciência baseada na confiança por outra fundamentada na transparência e na proveniência dos dados. Sua cultura epistêmica não impõe a obtenção de um fato científico como condição sine qua non para a comunicação de conhecimento novo, mas valoriza, sobretudo, o registro adequado da prática experimental seja qual for seu resultado – o que chamamos de matter of proof pela ênfase na documentação. Já na Ciência Comum (LAFUENTE, ESTALELLA, 2015), abordamos o caderno aberto de laboratório cidadão (CALC) prototipado por Antonio Lafuente e práticas de documentação de pesquisadoras-mediadoras do Medialab Prado, instituição pública madrilenha se autodenomina “laboratório cidadão”. Aqui, a crítica à noção de fato científico dialoga com o composicionismo latouriano ao compreendê-lo como um (importante) subconjunto da realidade que, no entanto, não deve se sobrepor aos debates políticos, mas conectar-se às “questões de interesse” (matter of concern). Nesta perspectiva, a modernização epistêmica fomentaria um “terceiro setor do conhecimento” que disputaria a governança antecipatória de assuntos tecnocientíficos (LAFUENTE, 2007). Nossa observação participante identificou que as práticas atuais de documentação tendem a reproduzir a lógica do campo da produção cultural que fomenta novos imaginários políticos, mas não inicia o ciclo de acumulação de conhecimento que o transformaria os laboratórios cidadãos em centros de cálculo (LATOUR, 2000). Os promotores de atividades tendem a reduzir a comunicação à divulgação de atividades para atrair participantes em potencial ou a prestação de contas, comprovando a realização de atividades. / We describe and analyze new epistemic cultures (KNORR-CETINA, 1999) that are being engendered by two emerging modes of science - Open Science and Common Science - that, despite numerous differences, converge on two aspects: the critique of scientific fact and their strategy of transforming laboratory notebooks into their main literary technology. We have adopted the notion of epistemic culture to operationalise our analysis of knowledge production systems strategies to configurate technologies, epistemic objects and subjects that, in turn, create effects of truth. To do so, we are inspired by laboratory ethnographies and Shapin and Shaffer's (1985) "three technologies" approach elaborated to explain how natural philosophers of the seventeenth century constructed the notion of scientific fact (matter of fact) so solid that it became synonym of science. Similarly, we aimed to understand how emerging modes of science seek to legitimize new ways of producing knowledge and disputing the very notion of science. In the contemporary Open Science movement, we approach open notebook science, proposed in 2006 by professor and researcher in Chemistry Jean-Claude Bradley as "a way of doing science in which - in the best possible way - you make all your research free and accessible to the public in real time" (BRADLEY, Sep 2010). We entered his "open laboratory" through documentary research that identified the open notebook as the main element of a complex ecosystem of open collaboration. Articulated with new social and material technologies, this literary technology aims to replace a science based on trust with one based on transparency and data provenance. Its epistemic culture does not impose a scientific fact as a sine qua non condition for knowledge communication, but values, above all, the adequate record of experimental practice whatever its outcome is - an epistemic culture that we have named a "matter of proof", given its emphasis on documentation. In Common Science (LAFUENTE, ESTALELLA, 2015), we investigated the open notebook of citizens' laboratory (CALC in spanish) prototyped by Antonio Lafuente and documentation practices of mediator- researchers at Medialab Prado, a public institution in Madrid that calls itself a "citizen's laboratory". Here, the critique of scientific fact dialogues with Latour´s compositionism since it is understood as an (important) subset of reality, which, however, should not supersede political debates, but rather relate to “matters of concern". In this perspective, the epistemic modernization process would foster a "third sector of knowledge" that would dispute the anticipatory governance of technoscientific subjects (LAFUENTE, 2007). Our participant observation has observed that current documentation practices tend to reproduce the logic of a cultural production field that fosters new political imaginaries, but does not initiate the knowledge accumulation cycle that would transform citizen laboratories into centre of calculation (LATOUR, 2000). Promoters tend to reduce communication to publicity of activities, attracting potential participants; or accountability, to prove that they carried out the projects.

L'objectif de mon travail de thèse était de développer des outils bio informatiques permettant d'améliorer la traditionnelle gestion de l'information scientifique au sein d'un grand centre de recherche et en particulier au sein d'une plateforme de génomique. Trois outils ont été développés: un cahier de laboratoire électronique, un système de gestion de l'information de laboratoire pour des applications de génomique dont le séquençage de nouvelle génération, ainsi qu'un système de gestion des échantillons pour de grandes bio-banques. Ce travail a été réalisé en étroite collaboration avec des biologistes, épidémiologistes et informaticiens. Il a également inclus la mise en place d'interactions entre les différents outils pour former un système informatique intégré. Les trois outils ont été rapidement adoptés par l'ensemble des scientifiques du centre de recherche et sont désormais utilisés au quotidien pour le suivi de toutes les activités de laboratoire mais aussi plus globalement pour les autres activités scientifiques du centre de recherche. Ces outils sont transposables dans d'autres instituts de recherche / The aim of my thesis work was to develop bioinformatics tools to improve the traditional scientific information management within a large research centre and especially within a genomics platform. Three tools have been developed: an electronic laboratory notebook, a laboratory information management system for genomics applications including next generation sequencing, as well as a sample management system for large biobanks. This work has been conducted in close collaboration with biologists, epidemiologists and IT specialists. It has also included the setup of interactions between the different tools to make an integrated IT system. The three tools have been rapidly adopted by all the scientists of the research centre and are now daily used for the tracking of all the laboratory’s activities but also more globally for the research centre’s other scientific activities. These tools are transposable in other research institutes