Doctoral Award

-




Detailed Information


Line


Project Information
Project Title: Assembly of reads from a mix of high-throughput sequencing technologies
Period: 

from: 2010-09-01


to: 2013-08-31
Principal Investigator(s):



BOISVERT, Sébastien
Co-Investigators:
Supervisors:



CORBEIL, Jacques


;


MARCHAND, Mario
Previous Investigators/Supervisors:
Institution:


Université Laval
Department:
Program:Doctoral Award - Frederick Banting and Charles Best Canada Graduate Scholarships 
Assigned PRC:DRA 
Primary Institute:Genetics 
Primary Theme:Biomedical 
Keywords:BIOINFORMATICS, BIOSTATISTICS, BIOSTATISTIQUES, DE NOVO SEQUENCING, GENOME ASSEMBLY, GENOME VARIATION, GENOMICS, PROTEOMICS, AND BIOINFORMATICS, GÉNOMIQUE, PROTÉOMIQUE ET BIOINFORMATIQUE, MUTATION DISCOVERY, RESEQUENCING 
Abstract:The treatment of diseases costs each Canadian a large amount of money. There is a genetic basis behind resistance to antibiotics and various genetics diseases. Genetic background accounts for predisposition to diseases, and the knowledge of the latter can promote better lifestyle. Sequencing technologies allow physicians to diagnose precisely the cause of some genetics disease, and thus explain patients the very cause of their sickness. When a resistant strain hits hard on a health care centre, the rapid identification of the pathogen agent is essential to avoid unnecessary lost of human lives. Genetic tests and pathogen detection kits are based on nucleic acid technologies, such as high-density micro-arrays and sequencing technologies. In the case of genetic diseases, these technologies allow the pinpointing of malfunctioning proteins, and the latter are addressed with tailored drugs, if any. There is a great need in Canada for people that can analyse the data produced by these DNA technologies -- we call them bioinformaticians. Owing to the complexity of the human genome and to the evolution of the associated technological medicine, new powerful tools are necessary to analyze the sheer volume of data. The knowledge of mutations that set the predisposition to known diseases, such as Alzheimer's disease, surely improves on the quality of life. The rapid detection and characterisation of disease agents reduces the chance of outbreak, and improves population health. In the next decade, sequencing technologies will allow the study of human genome variation through the sequencing of a thousand human genomes, offering a deep catalog of human genetic variation (http://1000genomes.org/). During my doctorate, I will develop tools to answer these important health questions in genomics. 


Funding Information
Fiscal
Year		Amount
2010-11

$35,000

Source: http://webapps.cihr-irsc.gc.ca/funding/

Comments

Post a Comment

Popular posts from this blog

A survey of the burgeoning industry of cloud genomics

-
Image
I like lists. Here is a list of companies in the cloud genomics industry. Table 1: Companies acting in the industry of cloud genomics. The list is in no particular order. Company Products People Founded Link GenoSpace, LLC - GenoSpace platform - John Quackenbush (CEO) 2011 https://www.genospace.com/ DNAnexus, Inc. - DNAnexus Platform - DNAnexus Platform SDK (a.k.a. dx-toolkit) - Serafim Batzoglou (co-founder) - Andreas Sundquist (co-founder and CTO) - a bunch of other famous people in the field 2009 https://dnanexus.com/ Seven Bridges Genomics, Inc. - IGOR - IGOR Python SDK - Igor Bogicevic (CTO) 2009 https://www.sbgenomics.com/ BGI - EasyGenomics - Xing Xu (Senior Product Manager) Introduced in 2012 https://www.easygenomics.com/ Illumina, Inc. - BaseSpace™ - BaseSpace API - Alex Dickinson (SVP of Cloud Genomics) Introduced in 2011 https://basespace.illumina.com/ Era7 Information Technologies SLU - BG7
Read more

Generating neural machine instructions for multi-head attention

-
  An animal can do training and inference every day of its existence until the day of its death. A forward pass is all you need.   Here is the current model configuration that I use for multi-head attention:         let sequence_length = 6;         let vocab_size = 20;         let n_embd = 64;         let num_heads = 8; You can see the full model here: https://github.com/sebhtml/novigrad/blob/8df6192829edd9cda3a221e12affa770fbda2a1b/src/models/mega_man_attention.rs The struct uses Embedding, MultiHeadAttention, Linear, Softmax: struct MegaManAttentionModel {     input_shape: Vec<usize>,     output_shape: Vec<usize>,     vocab_size: usize,     sequence_length: usize,     embedding: Embedding,     multi_head_attention: MultiHeadAttention,     linear: Linear,     softmax: Softmax, } The instructions generated by Novigrad are below. Notes: - INSTRUCTION    MatMul    t170 t166    t171     means that we do a matrix multiplication between tensors t170 and t166 and the result is wr
Read more

Adding ZVOL VIRTIO disks to a guest running on a host with the FreeBSD BHYVE hypervisor

-
On atlantis.domain (my FreeBSD BHYVE hypervisor host), I use these commands: Install FreeBSD on a 10G disk. vm create -s 10G guestname   vm install FreeBSD-12.1-RELEASE-amd64-memstick.img vm console guestname Add 8 30GB zvol-based disks vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname vm add -d disk -t zvol -s 30G guestname You will need to do vm poweroff guestname vm start guestname because the guest does not seem to see the 8 30GB without power cycling. (rebooting won't work) *** If you want the boot disk (the one create by "vm create") to be a zvol, you must edit the template: root@atlantis:~ # zfs snapshot tank/vm-bhyve@2020-06-11-2145 root@atlantis:~ # mount -t zfs tank/vm-bhyve@2020-06-11-2145 /tank/vm-bhyve@2020-06-11-2145 r
Read more