Mass Spectrometry Informatics in Systems Biology

Mass spectrometry (MS) became a standard tool for identifying metabolites in biological tissues, and metabolomics is slowly acknowledged as a legitimate research discipline for characterizing biological conditions. The computational analyses of metabolomics, however, lag behind compared with the rapid advances in analytical aspects for two reasons. First is the lack of standardized data repository for mass spectra: each research institution is flooded with gigabytes of mass-spectral data from its own analytical groups and cannot host a world-class repository for mass spectra. The second reason is the lack of informatics experts that are fully experienced with spectral analyses. The two barriers must be overcome to establish a publicly free data server for MS analysis in metabolomics as does GenBank in genomics and UniProt in proteomics. The workshop brought together bioinformaticians working on mass spectral analyses in Finland and Japan with the goal to establish a consortium to freely exchange and publicize mass spectra of metabolites measured on various platforms computational tools to analyze spectra spectral knowledge that are computationally predicted from standardized data. This book contains the abstracts of the presentations given in the workshop. The programme of the workshop consisted of oral presentations from Japan and Finland, invited lectures from Steffen Neumann (Leibniz Institute of Plant Biochemistry), Matej Oresic (VTT), Merja Penttila (VTT) and Nicola Zamboni (ETH Zurich) as well as free form discussion among the participants. The event was funded by Academy of Finland (grants 139203 and 118653), Japan Society for the Promotion of Science (JSPS Japan-Finland Bilateral Semi- nar Program 2010) and Department of Computer Science University of Helsinki. We would like to thank all the people contributing to the technical pro- gramme and the sponsors for making the workshop possible. Helsinki, October 2010 Masanori Arita, Markus Heinonen and Juho Rousu

Safeguarding against new privacy threats in inter-enterprise collaboration environments

Inter-enterprise collaboration has become essential for the success of enterprises. As competition increasingly takes place between supply chains and networks of enterprises, there is a strategic business need to participate in multiple collaborations simultaneously. Collaborations based on an open market of autonomous actors set special requirements for computing facilities supporting the setup and management of these business networks of enterprises. Currently, the safeguards against privacy threats in collaborations crossing organizational borders are both insufficient and incompatible to the open market. A broader understanding is needed of the architecture of defense structures, and privacy threats must be detected not only on the level of a private person or enterprise, but on the community and ecosystem levels as well. Control measures must be automated wherever possible in order to keep the cost and effort of collaboration management reasonable. This article contributes to the understanding of the modern inter-enterprise collaboration environment and privacy threats in it, and presents the automated control measures required to ensure that actors in inter-enterprise collaborations behave correctly to preserve privacy.

Probabilistic Inductive Querying Using ProbLog

We study how probabilistic reasoning and inductive querying can be combined within ProbLog, a recent probabilistic extension of Prolog. ProbLog can be regarded as a database system that supports both probabilistic and inductive reasoning through a variety of querying mechanisms. After a short introduction to ProbLog, we provide a survey of the different types of inductive queries that ProbLog supports, and show how it can be applied to the mining of large biological networks.

Describing syntax with star-free regular expressions

Koskenniemen Äärellistilaisen leikkauskieliopin (FSIG) lauseopilliset rajoitteet ovat loogisesti vähemmän kompleksisia kuin mihin niissä käytetty formalismi vittaisi. Osoittautuukin että vaikka Voutilaisen (1994) englannin kielelle laatima FSIG-kuvaus käyttää useita säännöllisten lausekkeiden laajennuksia, kieliopin kuvaus kokonaisuutenaan palautuu äärelliseen yhdistelmään unionia, komplementtia ja peräkkäinasettelua. Tämä on oleellinen parannus ENGFSIG:n descriptiiviseen kompleksisuuteen. Tulos avaa ovia FSIG-kuvauksen loogisten ominaisuuksien syvemmälle analyysille ja FSIG kuvausten mahdolliselle optimoinnillle. Todistus sisältää uuden kaavan, joka kääntää Koskenniemien rajoiteoperaation ilman markkerimerkkejä.

Developing Peer-To-Peer Web Applications

As the virtual world grows more complex, finding a standard way for storing data becomes increasingly important. Ideally, each data item would be brought into the computer system only once. References for data items need to be cryptographically verifiable, so the data can maintain its identity while being passed around. This way there will be only one copy of the users family photo album, while the user can use multiple tools to show or manipulate the album. Copies of users data could be stored on some of his family members computer, some of his computers, but also at some online services which he uses. When all actors operate over one replicated copy of the data, the system automatically avoids a single point of failure. Thus the data will not disappear with one computer breaking, or one service provider going out of business. One shared copy also makes it possible to delete a piece of data from all systems at once, on users request. In our research we tried to find a model that would make data manageable to users, and make it possible to have the same data stored at various locations. We studied three systems, Persona, Freenet, and GNUnet, that suggest different models for protecting user data. The main application areas of the systems studied include securing online social networks, providing anonymous web, and preventing censorship in file-sharing. Each of the systems studied store user data on machines belonging to third parties. The systems differ in measures they take to protect their users from data loss, forged information, censorship, and being monitored. All of the systems use cryptography to secure names used for the content, and to protect the data from outsiders. Based on the gained knowledge, we built a prototype platform called Peerscape, which stores user data in a synchronized, protected database. Data items themselves are protected with cryptography against forgery, but not encrypted as the focus has been disseminating the data directly among family and friends instead of letting third parties store the information. We turned the synchronizing database into peer-to-peer web by revealing its contents through an integrated http server. The REST-like http API supports development of applications in javascript. To evaluate the platform’s suitability for application development we wrote some simple applications, including a public chat room, bittorrent site, and a flower growing game. During our early tests we came to the conclusion that using the platform for simple applications works well. As web standards develop further, writing applications for the platform should become easier. Any system this complex will have its problems, and we are not expecting our platform to replace the existing web, but are fairly impressed with the results and consider our work important from the perspective of managing user data.

Two bracketing schemes for the Penn Treebank

The trees in the Penn Treebank have a standard representation that involves complete balanced bracketing. In this article, an alternative for this standard representation of the tree bank is proposed. The proposed representation for the trees is loss-less, but it reduces the total number of brackets by 28%. This is possible by omitting the redundant pairs of special brackets that encode initial and final embedding, using a technique proposed by Krauwer and des Tombe (1981). In terms of the paired brackets, the maximum nesting depth in sentences decreases by 78%. The 99.9% coverage is achieved with only five non-top levels of paired brackets. The observed shallowness of the reduced bracketing suggests that finite-state based methods for parsing and searching could be a feasible option for tree bank processing.

Linguistic grammars with very low complexity

We have presented an overview of the FSIG approach and related FSIG gram- mars to issues of very low complexity and parsing strategy. We ended up with serious optimism according to which most FSIG grammars could be decom- posed in a reasonable way and then processed efficiently.

Two bracketing schemes for the Penn Treebank

The trees in the Penn Treebank have a standard representation that involves complete balanced bracketing. In this article, an alternative for this standard representation of the tree bank is proposed. The proposed representation for the trees is loss-less, but it reduces the total number of brackets by 28%. This is possible by omitting the redundant pairs of special brackets that encode initial and final embedding, using a technique proposed by Krauwer and des Tombe (1981). In terms of the paired brackets, the maximum nesting depth in sentences decreases by 78%. The 99.9% coverage is achieved with only five non-top levels of paired brackets. The observed shallowness of the reduced bracketing suggests that finite-state based methods for parsing and searching could be a feasible option for tree bank processing.

Cooperative Replies to Unbelievable Assertions

We propose a dialogue protocol for situations in which an agent makes to another agent an assertion that the other agent finds impossible to believe. In this interaction, unbelievable assertions are rejected using explanations formed by logical interpolation and new assertions are being made such that all previous rebuttals are taken into account.

Enterprise architecture – the foundation for a strategy

Artikkeli selostaa kokonaisarkkitehtuurin käsitettä ja Kansallinen digitaalinen kirjasto -hankkeen kokonaisarkkitehtuurin laatimista. Kokonaisarkkitehtuuri on tietohallinnon strategisen suunnittelun ja johtamisen väline, mutta sillä on monia käytännöllisempia käyttötarkoituksia esimerkiksi tietojärjestelmien kehittämisessä. Kansallinen digitaalinen kirjasto on opetus- ja kulttuuriministeriön tavoitteena on varmistaa kulttuurin ja tieteen digitaalisten tietovarantojen tehokas ja laadukas hallinta, jakelu ja pitkäaikaissäilytys. Lisäksi hankkeessa edistetään kulttuuriperintö- ja asiakirja-aineistojen digitointia.