Animations & Physics

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Future movie and gaming industries will employ Finite Element Methods as they are far more numerically reliable and physically accurate than other methods, such as Finite Differences, a technique used for instance in cloth animation (as in Autodesk Maya). Currently we're working on two applicative fields: animation and engineering.

Answer this question: "how can I animate a water bottle, given an animation moving octopus?". The answer should be copy-paste, but we're not there yet: this is the morphology project. On the other hand, CNTs (Carbon Nanotubes) materials are interesting materials for several engineering fields (e.g., aerospace, clothing): see the finite elements project.

Bioinformatics

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Mobile (third-generation) genetic sequencing technologies, including Oxford Nanopore's MinION and SmidgION, fit in the palm of a hand and only require a USB outlet. Unfortunately, the development of data analysis tools for these technologies is in a nascent stage, impeding on the portability of these devices.

As genetic sequences require GBs if not TBs of data, we need to address scalability and portability issues, producing software that can, from a smartphone to a workstation, perform efficiently with limited RAM. Currently we are developing a library, libseq, and tools such as NanoPAL.

Older Projects

These projects are no longer maintained

HErCoOl

This work presents a novel error correction algorithm based on k-mer strings with their associated overlap graph, along with an open-source, multi-threaded, implementation. The algorithm, named HErCoOl (High-throughput Error Correction by Oligomers), needs minimal tuning, only an overall error rate and—optionally—information about the genome sizes.

Sequence

This work proposes an error correction method based on the de Bruijn graph that permits its execution on Gigabyte-sized data sets using normal desktop computers. The implementation makes extensive use of hashing techniques, and implements an A* algorithm for optimal error correction, minimizing the distance between an erroneous read and its possible replacement with the Needleman-Wunsch score.