Non-metric similarity search of tandem mass spectra including posttranslational modifications

AbstractIn biological applications, the tandem mass spectrometry is a widely used method for determining protein and peptide sequences from an “in vitro” sample. The sequences are not determined directly, but they must be interpreted from the mass spectra, which is the output of the mass spectrometer. This work is focused on a similarity-search approach to mass spectra interpretation, where the parameterized Hausdorff distance (dHP) is used as the similarity. In order to provide an efficient similarity search under dHP, the metric access methods and the TriGen algorithm (controlling the metricity of dHP) are employed. Moreover, the search model based on the dHP supports posttranslational modifications (PTMs) in the query mass spectra, what is typically a problem when an indexing approach is used. Our approach can be utilized as a coarse filter by any other database approach for mass spectra interpretation

Clustermethoden für Massenspektren in proteomweiten statistischen Analysen

Die Arbeit handelt von Clustermethoden für massenspektrometrische Analysen in der Biodiversitätsforschung. Alternativ zur Artenbestimmung mittels DNA-Barcoding wird die Analyse der Proteinzusammensetzung von Organismen verwendet. Die Mehrheit der Proteinanalytik basiert mittlerweile auf der sogenannten LC-MS/MS-Methode. Dabei wird eine Flüssigchromatographie (LC) als Trennmethode mit der Tandem-Massenspektrometrie (MS/MS) kombiniert. Tandem-Massenspektren, die aus detektierten Intensitäten von vorkommenden Massen bestehen, dienen zur Identifikation von Peptiden und Proteinen mittels Datenbanksuchalgorithmen. Neuartige unbekannte Peptide werden mittlerweile über fehleranfällige De-Novo-Peptidsequenzierungsalgorithmen detektiert. Alternativ zu Annotationsverfahren wird hier die direkte Clusteranalyse der Tandem-Massenspektren behandelt. Zwei Aspekte, die Clusteranalyse sogenannter Läufe, die tausende Spektren einer Proteinprobe umfasst, und die Clusteranalyse von einzelnen Tandem-Massenspektren werden untersucht. Eine Clusteranalyse sogenannter Läufe wird für mehrere reale Datensätze mithilfe der neuen Methode DISMS2 durchgeführt, die ohne Annotationen Distanzen zwischen MS/MS-Läufen bestimmt. Es handelt sich also um eine Alternative zum Vergleich von Peptidlisten, die auf der Identifikation von Spektren in Datenbanksuchen basieren. Die Parameter von DISMS2 sind frei wählbar, sodass die Auswahl der höchsten Peaks je Spektrum (topn), die Bingröße im Binning (bin), die Einschränkung bei dem Vergleich von Spektren auf zeitlich nahe Spektren (ret) mit ähnlicher Precursormasse (prec) und das Distanzmaß für Massenspektren (dist) mit einem frei wählbaren Schwellenwert (cdis) variieren. Zur Parameterwahl wird ein Vorgehen zur Optimierung angewandt, das das Bestimmtheitsmaß R2 eines nichtparametrischen Verfahrens zur Varianzanalyse verwendet. Zur Clusteranalyse von einzelnen Massenspektren wird ein bisher in der Literatur fehlender umfassender Vergleich von Algorithmen erstellt, die für Tandem-Massenspektren etabliert (CAST, MS-Cluster, PRIDE Cluster), für große Datensätze bekannt (hierarchische Clusteranalyse, DBSCAN, Zusammenhangskomponenten eines Graphen) oder neu (Neighbor Clustering) sind. Die Evaluierung basiert auf realen Daten und mehreren Gütemaßen

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Education and Social Work Handbook 2009

Tese de doutoramento em Arte Contemporânea, apresentada ao Colégio das Artes da Universidade de CoimbraEsta não é uma tese somente sobre o estatuto da imagem. A razão para isso é que nenhuma teoria é ou pode ser adequada à imagem e que o próprio estatuto provoca todas as ferramentas da reflexão teórica. Porque escolhi investigar imagens a partir da fotografia? Poderia falar de imagens a partir do desenho, da pintura e da tradição escultórica. Como inventar no espelho e aceitar os dogmas acerca da imagem, as definições que se tornaram convicções? Na escola de arte, embora tivesse habilidade para o desenho e para a pintura, meu interesse era nas imagens prontas. Uma tentativa de tirar o verniz das imagens é a chave daquilo que hoje chamo de a Imagem Emancipada. Vemos isso nos pintores, nos cineastas que se divergem e se vê através da tecnociência. Como amante da arte não posso desenvolver meu interesse pela técnica mais do que meu interesse pela crítica. O projeto de um futuro em Warburg: a antropologia da cultura ocidental em que a filologia, etnologia, história e biologia convergem com uma iconologia do intervalo, no qual o trabalho incessante é a memória social. A Imagem Emancipada são os clarões dentro das imagens que buscamos. Embora tivesse influência dos planos de cinema, as imagens que buscava construir, sempre vieram de minhas referências de pintores e suas soluções de espaço, cor e, por que não dizer, tempo. Foi no início dos anos oitenta, com a atmosfera de regresso à pintura e ao figurativismo, que a fotografia encontrou terreno fértil para se desenvolver rumo a novas direções.This is not a thesis that only covers image statute, and the reason is that no theory is, or can fit the image, and the thesis itself causes all theoretical reflection tools. Why have I chosen to investigate images from photograph? I could have talked about images from drawing, painting and sculpture tradition. How to invent in front of the mirror and accept the dogmas concerning the image and definitions that became convictions? At the art school, although I had the ability to draw and paint, my real interested was in finished images. An attempt to remove the varnish from images is the key of what I call today as Emancipated Image. We can see that in painters and filmmakers that diverge and see themselves through technology. As an art lover, I can not develop my interest for the critic. The project of a future in Warburg: western culture anthropology in which philosophy, ethnology, history and biology converge with an iconology of the recess, where the non stopping work is the social memory. Emancipated Image are the flash inside the images we seek. Although I had influence by cinema plans, the images I tries to build, always came from my references of painters and their solutions to space, color and why not mention, time. It was in the beginning of the 1980’s, with the return atmosphere to painting and to figuration, that photography found breeding ground to develop towards new directions

Education and Social Work handbook

2005 handbook for the faculty of Education and Social Wor