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Doctoral Student Position Available on Computational Pangenomics

We are looking for a talented and motivated PhD student with a special interest in algorithms and data structures and their application in bioinformatics (sequence analysis). The PhD student will be positioned at CWI within the "Algorithms for PAngenome" (ALPACA) network (website) funded by the European Commission through the Horizon 2020 Marie Sklodowska-Curie ITN Programme.

The move from sequence- to graph-based pan-genome data structures is unavoidable when seeking to exploit the wealth of genetic data, instead of having devices massively congested. Putting the paradigm shift (from sequences to graphs) in effect requires new ways of thinking about genomes, as well as computer programs and mathematical models that reflect this. However, developing, maintaining and computationally/statistically exploiting graph-based pan-genomes requires skills that common-day education does not yet provide. The goal of this project is to train a new class of researchers who are able to deal with the (exabyte-scale) masses of genome data in terms of the progressive, graph-based approaches the research of this project deals with.

Objectives: Comparing pan-genomes amounts to comparing two graphs, generalizing the idea to align two genomes. We aim at developing algorithms and software for 'whole-pan-genome alignment'. Though for aligning two networks approaches already exist, they do not address the peculiarities of pan-genome graphs, in, for example, de Bruijn graph or variation graph based pan-genomic data structures. We will address these particular issues in full detail. In addition, we will study phylogenetic relations within and across pan-genomes. In applications, we will compare also 'pan-transcriptomes', e.g. liver cell with colon pan-transcriptome, and microbiomes, integrated into pan-genomes, so as to accurately identify the commonalities and differences between the two entities.

Supervised by: Solon P. Pissis (website) and Leen Stougie (website).

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26-11-2020 Centrum Wiskunde & Informatica
Scientific Programmer

As part of the European Next Generation Internet project, the job is to work on a new architecture for communication over the Internet. This project is a rip-and-replace effort of the BSD-style socket by an innovative abstraction: connectors. Connectors are based on decades of research performed at the CWI. Over the course of at least two years, building further on an existing reference implementation, we will research & develop a distributed and fault-tolerant version of the connector communication mechanism, and will work together with the Internet community on standardization. The development is fully public and open source (EUPL). There is lots of freedom to experiment and do independent research, that could result in the development of compiler optimizations, protocol language extensions, or security features.

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26-10-2020 Centrum Wiskunde & Informatica
PhD student on "Models for adaptable ship design for uncertain transition paths"

Recently, the International Maritime Organization (IMO) has agreed to reduce CO2 emissions of shipping by 40% in 2030 and even further by 2050. This raises tremendous challenges related to the energy transition and the transition towards autonomous ships. Ships currently designed will still be around after the transitions, requiring multiple modifications in the ship and system layout to stay relevant.

The overall goal of this project is to develop new quantitative models and solution algorithms that advance the ship design process by reducing the impact and costs of uncertain future modifications in the control of systems, the ship topology, and in particular, the routing of cables, ducts and pipes. In this context, specific challenges include (1) the limited amount of space for cables, ducts and pipes, and (2) the assembly order. To this end, we aim to extend current routing methods by including relevant aspects such as space-limitations, removability, replaceability, accessibility and uncertainty. We will also develop a new assessment approach for the assembly order.

The methods-to-be-developed will allow reservations to be made for future implementations under uncertainty and without sacrificing available space unnecessarily. The developed methods will empower the maritime sector to seamlessly transition from ships nowadays to autonomous ships with zero emissions. The analyses will be done both theoretically, as well as practically in case studies.

Position
We offer a full-time 4-years PhD position. The student will become a member of the Stochastics group at the Center for Mathematics and Computer Science (CWI), and get his/her PhD degree from the Vrije Universiteit Amsterdam. The student will be part of a research team and will be working closely together with researchers from the Vrije Universiteit Amsterdam and with other PhD candidates at the TU Delft.

1 sollicitatie
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26-10-2020 Centrum Wiskunde & Informatica
Tenure track position in multimedia systems and human-computer interaction

The Distributed and Interactive Systems research group focuses on modeling and controlling complex collections of media objects (including real-time media and sensor data) that are interactive and distributed in time and space. The research group focuses on facilitating and improving the way people use interactive systems and how people communicate with each other, by combining data science with a strong human-centric, empirical approach to understand the experience of users. This enables the group to design and develop next generation intelligent and empathic systems. The Distributed and Interactive Systems research group focuses on modeling and controlling complex collections of media objects (including real-time media and sensor data) that are interactive and distributed in time and space. The research group focuses on facilitating and improving the way people use interactive systems and how people communicate with each other, by combining data science with a strong human-centric, empirical approach to understand the experience of users. This enables the group to design and develop next generation intelligent and empathic systems.

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16-10-2020 Centrum Wiskunde & Informatica
Programmer for dummies.

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16-10-2020 Centrum Wiskunde & Informatica