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 Congratulations to the participants of the hackathon!

Congratulations to all the participants of the hackathon! This year, the partipants had to use machine learning technique to predict the gestational age based on a dataset of blood transcriptomics from pregnant mothers. This challenge was taken from a worldwide competition organized by the Dream Challenges. 
https://www.synapse.org/#!Synapse:syn18380862/wiki/590485

Jules Lambert and Matthew Salaciak came up with the best solutions, being able to predict within an error margin of 6 weeks the gestational age. This puts them among the top 10 competitors for the world wide challenge, an impressive result in just 24 hours.

Thank to everyone who participated, who helped organize, and the to StartpFest for inviting us to their HackerFest!






 Hackathon!

Our annual hackathon will take place this Friday from July 12th to July 13th at the park Jean-Drapeau during the StartupFest’s HackerFest.

You’ll have just under 24 hours to use machine learning techniques to solve a molecular biology problem. Winners will get the glory of winning the annual MonBUG hackathon, a t-shirt (medium size only), and an opportunity to advance scientific knowledge.

If you’d like a free ticket to attend, just contact one of the organizers. Otherwise, you can register through the HackerFest for 12.76$, taxes included, using the following link.
https://www.eventbrite.ca/e/mon-bug-hackerfest-2019-tickets-63773636664

There are no requirements to attend. Just bring a laptop. If you can pre-install Python and some machine learning libraries to save time. We should post some links to the recommended libraries and to some tutorials prior to the hackathon.

This is our fourth year participating in the HackerFest. We had great fun the last years. The organization was always stellar, with spectacular locations. The event should take place in outdoor tents, with all services provided. Spending the night is optional, but if you do, it will be a safe and fun environment. There should be food available throughout the even, but to be on the safe side, you can always bring some of your own, and a sleeping bag if you like.

Feel free to ask any questions you have on Meetup.
http://www.meetup.com/monbug

Looking forward to seeing you all on Friday!






 10 year anniversary!

Please join us to celebrate MonBUG’s 10 year anniversary on Wednesday May 29th at 5pm at IRCM. The evening will start with a panel discussing the evolution of bioinformatics in Montreal in the last decade and will be followed by a cocktail. A big thanks to our sponsors: IRCM, McGill Department of Human Genetics, Streamline Genomics, IVADO & Génome Québec!

Register at: http://www.meetup.com/monbug

We’d also like to extend a warm welcome to our two newest sponsors.







 September meeting

We’re back for another year!
Register for the next meeting at http://www.meetup.com/monbug, or by sending an email to register@monbug.ca.
Gabrielle Perron from Dr. Najafabadi’s lab in McGill’s Human Genetics Department will be presenting her research.
Chelsea Douglas, head of the documentation and support teams at Plotly will be presenting to us the capabilities of Plotly.

If you’d like to give a talk, just contact any one of the organizers.
We still have some free t-shirts to give away to presenters, so volunteer now before we run out of t-shirts!

Agenda
17:00 – 17:05 Introduction and community announcements
17:05 – 17:45 Modelling the regulatory networks that govern mRNA stability and their implication in cancer, Gabrielle Perron
17:45 -18:05 Sandwichs and refreshments
18:05 -18:30 Introduction to Plotly’s Dash: a pythonic web application platform, Chelsea Douglas






 Summer hackathon

Registration is now open for our annual summer hackathon!
To register, click on the link below.
https://www.eventbrite.ca/e/monbug-summer-hackathon-hackerfest-tickets-46443561944

The StartupFest has once again generously agreed to host our hackathon this year, in the context of their HackerFest, that follows the StartupFest.
The registration cost is 12.76$, taxes included, which is a symbolic contribution to the cost of setting up the event, and includes food (I believe).
The organizers have given us a few free tickets.
Just ask us for one, and we’ll send you the link to register for free, until the free tickets are exhausted.
Exceptionally this year, we also have free tickets for the StartupFest itself, provided by both the organizers of the StartupFest and our sponsor, the local bioinformatics startup, Streamline Genomics (http://www.streamlinegenomics.com/)
They’re sold for about 500$ each, I think.
We’ll give them to the first person, registered in the hackathon, to claim them.
The only condition to claiming a free ticket is that you must use it, or you’re depriving someone else of a free ticket.

This year, the hackathon will take place in a park, on a peninsula in front of the Old Port.
It should be a spectacular location.
The problem we will tackle will be a machine learning problem involving a current molecular biology dataset.
You’ll have 24 hours to program a solution.
The winner(s) will get the glory of winning the MonBUG summer hackathon, an opportunity to advance science and a MonBUG t-shirt.

The last 2 years were tremendous fun, and the organization was stellar.
We had huge outdoor tents, so I’m hoping the 2018 edition will be as successful.

Don’t hesitate to ask any questions you have, in the comments section or directly to one of the organizers.
We’ll open a Slack channel the day before the hackathon.

To stay posted on all of MonBUG’s events, register on http://www.meetup.com/monbug.






 May meeting

We have another great line-up.
Dr. Lavallée will be coming from Ottawa to present to us his lab’s research. Jean Monlong will be explaining to us the ins and outs of R Markdown. To learn more about Dr. Lavallée’s research, consult his lab’s website, where he discusses his exciting research applying computational methods, including machine learning, to proteomics data. https://med.uottawa.ca/bmi/people/lavallee-adam-mathieu

We have more plans for the next months, including a hackathon, and getting our t-shirts for the summer. Only speakers get t-shirts, so if you want one, volunteer to give a talk.

Wednesday, May 9th, Room André-Barbeau, IRCM
Register for the meeting at http://meetup.com/monbug or by sending an email to register@monbug.ca.

Agenda
17:00 – 17:05 Introduction and community announcements
17:05 – 17:45 Functional 5′ UTR Motif Discovery with LESMoN: Local Enrichment of Sequence Motifs in Biological Networks, Dr. Lavallée
17:45 -18:05 Sandwichs and refreshments
18:05 -18:30 Introduction to R Markdown, Jean Monlong

“I will present the Markdown syntax and how to combine it with the R Markdown package to produce dynamic reproducible reports. R Markdown makes an analysis workflow much more pleasant and saves a lot of time. It’s great for many applications: personal lab notes, data exploration, sharing results with collaborator/supervisor, publishing code with a manuscript.
I’ll show how to convert a simple document with R code into HTML reports, PDF slides and other formats. I’ll also share a few tricks that made my experience easier.”






 Spring meeting

Register on http://meetup.com/monbug, or by sending an email at register@monbug.ca.
The next meeting will be on Wednesday, March the 14th, from 17:00 to 18:45 in the André-Barbeau room, at the IRCM.

MonBUG is back with the arrival of spring!
This meeting will be all about R.

Mathieu Lajoie, PhD, will be showing us how he uses R in his genetic analyses. Selin Jessa, author of the R package chromswitch, will be walking us through the steps to submit our own package to Bioconductor, the R repository for bioinformatics packages.

Agenda
17:00 – 17:05 Introduction and community annoucements
17:05 -17:45 “Getting reliable estimates of tumour purity to improve downstream analyses”, Mathieu Lajoie, PhD, Watson lab
17:40 – 18:05 Break, with snacks and refreshments
18:05 – 18:45 An introduction to Bioconductor package development, Selin Jessa, Kleinman lab

Abstract of Mathieu’s presentation
“Getting reliable estimates of tumour purity to improve downstream analyses. Solid tumour samples are usually contaminated with a highly variable fraction of infiltrating lymphocytes and stromal cells.In this presentation I will describe different approaches to estimate the cancer cell fraction and discuss how this can impact RNAseq and copy number analysis, using TCGA data. R code snippets included.”

We’re always looking for enthusiastic presenters. MonBUG is meant as an informal forum for bioinformaticians to share their research, so don’t be shy about presenting.
Also, if you’re looking for a job, or offering a job, it’s also a great place to network. We’ll even give you the floor to sell yourself at the beginning of the meeting, if you want.






 October meeting

We have another great line-up.
To register, and for all the details, go to Meetup, http://meetup.com/monbug.

Sandrine Moreira, who did her PhD in bioinformatics at Université de Montréal, will be coming from Columbia University in New York to present her post-PhD research on non conventional microbial genomes.
Rached Alkallas will be presenting his research published just this month in Nature Communications, “Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease.”

Agenda
17:00 – 17:05 Introduction and community announcements
17:05 – 17:35 “Decryption of mitochondrial genes in diplonemids by RNA editing and trans-splicing”, Sandrine Moreira, post-PhD Landweller lab
17:35- 18:00 Break, with snacks and refreshments
18:00 – 18:30 “Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer’s disease.”, Rached Alkallas, PhD student Najafabadi and Watson lab

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Don’t forget to subscribe to our revived YouTube channel, which we will now be updating regularly.
https://www.youtube.com/channel/UCpLqBEa6o6nmoI9zLtOHCPw

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Here is the link to Rached’s article.
https://www.nature.com/articles/s41467-017-00867-z

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Here is a summary of the talk that will be given by Sandrine.

Decryption of mitochondrial genes in diplonemids by RNA editing and trans-splicing

Thanks to new high throughput sequencing technologies and automatic annotation pipelines, proceeding from an eppendorf tube to a genbank file can be achieved in a single mouse click or so, for some species. Others, however, fiercely resist bioinformaticians with their confounding genomic complexity. Ciliates and Diplonemids are one of them. My work is centered on the discovery of new strategies for encrypting genetic information in eukaryotes with unconventional genome architecture, and the identification of molecular decoding processes. I will essentially describe the work performed on diplonemids during my Ph.D. Diplonemids are a group of poorly studied marine protists. Unexpectedly, metagenomic studies have recently ranked this group as one of the most diverse and the most cosmopolitan in the oceans. Yet, their most distinctive feature is their multipartite mitochondrial genome with genes in pieces, and encryption by nucleotide deletions and substitutions. In contrast to all other organisms, their mitochondrial genes are systematically fragmented in pieces (modules) that are scattered across hundreds of small circular chromosomes. Gene pieces are transcribed independently into RNAs, that are then trans-spliced in the correct order, resembling a genomic jigsaw puzzle. Genes are further decrypted at the RNA level through RNA editing by polyuridylation at the junction of gene pieces and substitutions of A-to-I and C-to-T. Such a diverse arsenal of mitochondrial post-transcriptional processes is highly exceptional.

Using a bioinformatics approach, I have first reconstructed the mitochondrial transcriptome from RNA-seq libraries, second completed the chromosome catalogue from DNA-seq libraries, and finally annotated mitochondrial chromosomes. Genes were barely recognizable due to their extreme divergence. The gene complement contains 10 protein genes of the respiratory chain, the small and large ribosomal subunits and six new genes including one that presents alternative trans-splicing isoforms. Moreover, by comparing DNA and mature RNA sequences, we discovered that the RNA message is edited. In total, there are 216 uridines added in 14 genes with up to 29 U insertions, and 114 positions edited by deamination (A-to-I or C-to-T) among seven genes.

In order to identify the machinery that processes mitochondrial RNAs, the nuclear genome has been sequenced. I have then assembled and annotated the genome. This machinery is probably unique and complex because no cis signal or trans actor typical for known splicing machineries have been found. I have identified promising protein candidates that are worth to be tested experimentally, notably RNA ligases, numerous members of the PPR family involved in plants RNA editing and deaminases.

During my thesis, we have identified new types of post-transcriptional RNA processing in diplonemid mitochondria and identified new promising candidates for the machinery. A system capable of joining precisely or editing RNAs could find biotechnological applications. From an evolutionary perspective, the discovery of new molecular systems gives insight into the process of gene recruitment, adaptation to new functions and establishment of complex molecular machineries.






 September meeting

We’re back for another year!
We’d first like to thank the McGill Department of Human Genetics, and its chair Dr. Shoubridge, for renewing their sponsorship for another year.

We have a great line-up.
To register for the meeting, go to our Meetup page, http://meetup.com/monbugm, or send an email to register@monbug.ca if you’re allergic to Meetup.

Agenda
17:00 – 17:05 Introduction and community announcements
17:05 – 17:35 Establishing a link between CNVs and IQ, Guillaume Huguet and Catherine Schramm
17:35- 18:05 “Untangling the hairball: fitness based asymptotic reduction of biological networks”, Thomas Rademaker
18:05 – 18:25 Break, with snacks and refreshments
18:25 – 19:00 R tutorial, Mathieu Lajoie

Guillaume will be establishing the link between copy-number variants and general intelligence in unselected populations.

It’s a fascinating subject.
Time will unfortunately be limited for such a vast subject, but it will be interesting to have a debate about what links can be established between genomic data, and intelligence in the general population.

You can read more about Thomas research in his recently published article.
https://arxiv.org/abs/1707.06300

Mathieu’s R tutorial will be covering the following subjects.
1) Recovering multi-nucleotide variants from incorrectly processed NGS data.
2) Converting variants to a different genome build.

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As always, if you’d like to give a talk, either to present your own research or to give a tutorial, don’t hesitate to contact one of the organizers. We’re always looking for enthusiastic presenters.

We’re also relaunching our YouTube channel this year. We’re looking for a volunteer to film the presentations and manage the channel. If you’re interested, contact us.

We do occasionally get contacted both by job seekers, and people offering jobs.
Let us know if you’re looking or offering a job, to see if we can help match you.

Finally, if you have a preference for the time of the meetings, you can participate in our poll. https://www.meetup.com/MonBUG/polls/1240417/






 Congratulations to the winners of the MonBUG 2017 summer hackathon!

Congratulations to the winners of the MonBUG 2017 summer hackathon!


The winners are Loic Bruneau, Laurence Liang, Stephen Lu, Johann Akré, Jules Lambert, and Thomas Rademaker.

In just 24 hours they were able design and write a program able to classify DNA variants according to their functional impact,
by parsing the existing scientific literature on the variants, and training their model on a subset of variants that had been classified.

It was great fun, and a great team.
Thank you to the organizers of Startupfest and Hackerfest for inviting us.
We’ll definitely be back next year.

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Our regular meetings will start again in September.
We already have a few good talks lined up.
As always, if you’d like to give a talk, either to present your own research or to give a tutorial, don’t hesitate to contact one of the organizers.
We’re always looking for enthusiastic presenters.

To register for our meetings, just register on http://meetup.com/monbug.