590 stories
·
24 followers

Computational postdoc opening at UC Davis!

1 Comment and 2 Shares

We are currently soliciting applications for computational postdoctoral fellows to undertake exciting projects in computational biology/bioinformatics jointly supervised by Dr. Titus Brown (http://ivory.idyll.org/lab/) and Dr. Fereydoun Hormozdiari (http://www.hormozdiarilab.org/) at UC Davis.

UC Davis is a world class research institution with a strong genomics faculty. In addition to being part of Dr. Brown and Dr. Hormazdiari's labs, the postdoc will be able to participate in Genome Center activities. Potential collaborators include Megan Dennis, Alex Norde, and Paul and Randi Hagerman. UC Davis is close to the Bay Area and there will be opportunities to connect and collaborate with researchers at Berkeley, Stanford, and UCSF as well.

Davis, CA is an excellent place to live with good food, great schools, nice weather, non-Bay-Area housing prices, and a bike-friendly culture.

---

The successful candidate will undertake computational method and tool development for better understanding the contribution of genetic variation (especially structural variation) on changing the genome structure. In collaboration with the members of both labs, the postdoctoral candidate will also be building models for predicting the changes in gene expression based on variants (especially CNV) and performing a comparative study of genome structures in multiple tissues/samples using HiC data.

This opportunity requires developing novel computational algorithms and machine learning methods to solve emerging biological problems. The technical expertise needed include strong computational background to develop novel combinatorial, machine learning (ML) or statistical inference algorithms, with strong programming capabilities and a general understanding of the concepts in genomics and genetics.

Candidates are guaranteed funding for two years and will be strongly encouraged to apply for external funding in the second year of their postdoc to make a successful transition to independent investigator.

Some of the projects to work on include but are not limited to:

  • Computational methods to discover and predict the structural variations (SV) which will result in significant modification of genome structure. It is been shown recently that structural variation which results in modification of TAD (Topologically Associating Domains) can result in genetic diseases. As part of this project we are trying to develop methods which would predict which SVs will result in such a significant modification and potentially build a method for ranking/scoring SVs based on their pathogenicity in disease such as autism and cancer.
  • Study the effect of SV/CNVs which result in significant changes of genome structure during (great ape) evolution and associated with changes in gene expression for each of these species as a result of such variants.
  • Develop computational tools for finding conserved and significantly differentiated TADs in two more samples (from different cell types or species) using HiC data, with application to data from different tissues and/or species.

The start date for this position is flexible, although we hope the successful candidate can start before Sep 1, 2017.

Suggested candidate background:

  • Ph.D. in computer science, computational biology or related fields
  • Excellent programming skills in at least one language (C/C++, Java or Python)
  • Strong written/oral presentation skills
  • Enthusiasm for genomics-related problems
  • Knowledge of next-generation sequencing technologies and HiC data is a plus.

Interested candidates should send their CV and a research statement to Fereydoun Hormozdiari (email: fhormozd[at]ucdavis.edu) and Titus Brown (email: ctbrown[at]ucdavis.edu).

We will begin review of applications on Feb 1, 2017.

Read the whole story
luizirber
16 days ago
reply
Come work with us! =]
Davis, CA
codersquid
37 days ago
reply
chicago
Share this story
Delete

2017 - A two-week summer workshop on high-throughput sequencing data analysis!

1 Share

I am pleased to announce that we will be running a two-week summer workshop on analyzing high-throughput sequencing data! This workshop will run from June 26-July 8th, 2017, and it is an continuation of the two-week NGS workshop run at Michigan State University since 2010. (You can read about the 2015 workshop here.)

With our move to UC Davis, this year we will be able to take 3-4x as many applicants as in previous years!


ANGUS: Analyzing High Throughput Sequencing Data

June 26-July 8, 2017

University of California, Davis

  • Zero-entry - no experience required or expected!
  • Hands-on training in using the UNIX command line to analyze your sequencing data.
  • Friendly, helpful instructors and TAs!
  • Summer sequencing camp - meet and talk science with great people!
  • Now in its eighth year!

The workshop fee will be $500 for the two weeks, and on-campus room and board is available for $500/week. Applications will close March 17th. International and industry applicants are more than welcome!

Please see http://ivory.idyll.org/dibsi/ANGUS.html for more information, and contact dibsi.training@gmail.com if you have questions or suggestions.


--titus

Read the whole story
luizirber
16 days ago
reply
Davis, CA
Share this story
Delete

Instructor training for teaching computational workshops

1 Share

As part of our Summer Institute in Data Intensive Biology, we will be running a week-long instructor training from June 18 to June 25 at the University of California, Davis.

The instructor training will include the following --

  • Hands-on training in good pedagogical practice!
  • Become a certified Software/Data Carpentry instructor!
  • Learn to repurpose and remix online training materials for your own needs!

This workshop is intended for people interested in teaching, reusing and repurposing the Software Carpentry, Data Carpentry, or Analyzing Next-Generation Sequencing Data materials. We envision this course being most useful to current teaching-intensive faculty, future teachers and trainers, and core facilities that are developing training materials.

The workshop fee will be $350 for the week. Applications will close March 17th.

Please see http://ivory.idyll.org/dibsi/instructor-training.html for more information, and contact dibsi.training@gmail.com if you have questions or suggestions.


--titus

Read the whole story
luizirber
16 days ago
reply
Davis, CA
Share this story
Delete

O Espírito Santo de hoje é o Brasil de amanhã

2 Shares

caos no espírito santo 850x491 O Espírito Santo de hoje é o Brasil de amanhã

 

O Espírito Santo fez o dever de casa. O governador Paulo Hartung saneou o Estado. Equilibrou as contas públicas. É exemplo a ser seguido pelos outros Estados. No ano passado esse era o discurso dos jornalistas, dos economistas, dos experts. Silenciaram nos últimos dias. Silenciaram também 87 pessoas, assassinadas desde a última sexta-feira.

A violência no Espírito Santo está diretamente ligada aos planos de austeridade impostos pelo governo estadual nos últimos anos. Como o crescimento da violência no Brasil - e do desemprego e do desespero - está diretamente ligada aos planos de austeridade impostos pelo governo federal desde 2014. Quando os arrochos nacional e local se somam, as vítimas se multiplicam.

O que os 10.300 policiais militares do Espírito Santo querem? É a PM com o mais baixo piso salarial do país, R$ 2460,00. A média do Brasil é R$ 3980,00. Eles não têm aumento há sete anos, e há três anos o governo estadual nem repõe as perdas da inflação. Os PMs também reivindicam a renovação da frota de veículos, a melhora das condições do hospital da polícia, e a compra de coletes à prova de bala, que estariam em falta.

É fácil de argumentar que não devia existir Polícia Militar, só civil. Mas vamos deixar isso para lá no momento, e reconhecer que o que os PMs do Espírito Santo pedem não é muito. É muito pouco: salário mais próximo da média nacional e condições mínimas para fazer seu trabalho, que é bem perigoso.

Em vez de negociar com a polícia militar, o governador pediu ao governo tropas do exército. Chegaram lá e tomaram tiros dos bandidos. Vitória segue paralisada, comércio e escolas fechadas, ônibus não circulam. Os turistas fogem das praias capixabas. Os corpos se acumulam no departamento médico legal, que não dá conta de tanta morte. A Polícia Civil está avaliando se adere à greve. E as esposas dos PMs seguem protestando nas portas dos quartéis.

Qual a proposta concreta do governo do Espírito Santo para a PM? Nenhuma. A questão é que se o governador cede aos PMs, terá que ceder aos policiais civis. E depois ao resto do funcionalismo.

O governador Paulo Hartung, do PMDB, começou essa política de arrocho já em 2015. Mesmo tendo os custos com funcionalismo bem abaixo do limite da Lei de Responsabilidade Fiscal. Naturalmente não faltou dinheiro para outras atividades do governo - desonerações a grandes empresas, obras eleitoreiras etc. Foi louvado, e até considerado um bom candidato à presidência da República.

Tem outra questão. Se o governo começa a ceder às demandas dos funcionários do Estado, daqui a pouco vai ter que ceder às demandas da população que é atendida pelo Estado. Do povão em geral, que precisa de giz na sala de aula e merenda no intervalo, vaga e leito no hospital, paz para ir e voltar do trabalho, e outras coisas simples assim. E isso é exatamente o que os administradores do país, dos estados e das cidades se recusam a nos dar. Não que nada disso seria "dado", porque que a gente já paga bem caro por isso tudo.

Nos últimos tempos ouvimos muito o argumento de que "o Brasil está quebrado" - o país, os estados, as cidades - o que exigiria medidas duras. "Herança Maldita" que exige cortar na carne, no osso. Nos salários, aposentadorias, direitos.

Na verdade, a conta é outra. O Brasil não está quebrado. O que o Brasil não pode mais se permitir é ter 99% dos brasileiros pagando muitos impostos, e o 1% dos brasileiros mais ricos pagando quase nada de impostos. Nossos milionários pagam pouco imposto de renda como pessoa física, pagam pouco imposto de herança, e como pessoa jurídica pagam também pouquíssimo imposto. Além disso as grandes empresas têm toda espécie de benefícios do Tesouro Nacional. Empréstimos de pai para filho do BNDES e BB, dívidas perdoadas, "desonerações" etc.

Ontem o Espírito Santo já contava 75 assassinatos, depois de três dias de greve da PM. Ontem o Itaú, o maior banco do Brasil, publicou o seu balanço. No ano de 2016, com a maior recessão que o país já viveu, o Itaú lucrou R$ 22 bilhões. Se esse lucro fosse taxado em 50%, ainda assim seria um belíssimo lucro. O que dá para fazer com R$ 11 bilhões? Escola, estrada, esgoto.

Esse é só um de muitos exemplos possíveis. Se o Brasil não der um presente bilionário às empresas de telecomunicações, como quer o governo, também teremos um bom dinheiro para pagar policiais, professores, enfermeiras. É a Lei Geral das Telecomunicações, que está para ser aprovada, e transfere para Oi e outras teles um valor tão grande, que nem se sabe exatamente quanto é. O governo diz que é R$ 17 bilhões, o Tribunal de Contas da União diz que é R$ 105 bilhões...

E por aí vai.

Ainda podemos botar na conta o tanto que se desvia na corrupção, que sabemos não é pouco. E o que se sonega, que sabemos que é muito. Segundo a Procuradoria da Fazenda Nacional, a sonegação de impostos no Brasil pode chegar a R$ 500 bilhões por ano. Para você comparar: o Bolsa-Família custa R$ 27 bilhões por ano.

A próxima vítima será o Rio de Janeiro. O estado está para assinar um acordo com o governo federal que inclui um pacotão de arrocho para cima dos funcionários públicos do estado, inclusive policiais. Uma das exigências do governo é a privatização da Cedae, a companhia estadual de águas e esgotos, o que será feita por Pezão, vice de Sérgio Cabral...

As políticas de "austeridade" no mundo todo deram errado e estão dando muito errado aqui também. Em 2017 o Brasil não vai crescer nada. O que o poder público nos oferece são serviços públicos cada vez piores, chegando à insanidade de termos 87 mortos em quatro dias no Espírito Santo.

Na prática, os brasileiros pobres e da classe média sustentam as benesses dos brasileiros super ricos, a mamata dos sonegadores e a sujeira da corrupção. Então falta dinheiro para cobrir as necessidades básicas da população. Se a gente parar de sustentar os ricos, o Brasil equilibra as contas rápido.
E se além disso os ricos passarem a pagar a sua parte, o Brasil rapidamente vai ser tornar... rico.

Vamos encarar a realidade: tem dinheiro de sobra para o Brasil ser um país melhor para todos. Esta é a única pauta que importa, a pauta que precisamos impôr a cada dia, e também a cada nova eleição. Basta cobrar mais imposto de quem pode pagar mais, o que nunca aconteceu. Bater forte na sonegação e nos sonegadores, o que nunca aconteceu. E bater forte na corrupção e nos corruptores, o que começou a acontecer - mas só começou e agora, pelo jeito, parou.
Na prática, o que está sendo feito pelos nossos governantes, e apoiado pelos economistas, colunistas, especialistas, é o contrário do que precisa ser feito. O Espírito Santo de hoje é o Brasil de amanhã. E a próxima vítima é você.

http://r7.com/hoZc

O post O Espírito Santo de hoje é o Brasil de amanhã apareceu primeiro em André Forastieri.

Read the whole story
vitormazzi
13 days ago
reply
Brasil
luizirber
17 days ago
reply
Davis, CA
Share this story
Delete

What to do

1 Share

Read the whole story
luizirber
17 days ago
reply
Davis, CA
Share this story
Delete

DIB Lab Retreat to Yosemite, February 2017

1 Comment

This past weekend, all of us in Titus Brown’s Data Intensive Biology (DIB) lab went to Yosemite Bug, which is just outside Yosemite National Park, for our first (annual?) lab retreat. We had a great time! I personally found it inspiring to gather thoughts on the direction of research in the lab, ask questions about what everyone else is working on, and think about how my research goals fit into the larger picture of the lab.

Here are some notes from the weekend in case anyone is interested. Please comment and ask questions. Further discussion is welcome!

image-uploaded-from-ios-2 20170204_132517_32587306361_o
Photos by Harriet Alexander (left – Camille Scott looking far yonder) and Lisa Cohen (right)

Retreat

In October, about 4 months prior, we all agreed on location, date and began planning (gathering info, booked rooms and conference space from the resort). About one week prior, we had a brainstorming meeting about the schedule and what we would discuss.

Everyone drove up (~3.5 hrs from Davis) to Yosemite Bug on Friday. We discussed lab business on Sat and Sunday with some time in the middle to enjoy the outdoors and discuss with each other in an informal setting. The idea was to stimulate discussions about the lab (e.g. research, culture and career development) in a context outside the lab. We wanted it to be different than a conference. A retreat would just be our group, more broad/casual than regular lab meetings, to discuss the big picture of the lab’s research direction.

Saturday morning, presentations

To open, Titus identified major themes in the lab right now:
* Expect many big samples continuously arriving,
* Sketch data structures and online/streaming algorithms are good,
* Pre-filtering is good, especially when each step has low false negative rate
* Decentralized is good

Throughout the morning, there were presentations from the major projects in the lab. Presentations were 10 min each with 5 min discussions. Some hot topics bled over to be ~30 min each. These were informal talks with markers and flip chart only (no slides or projector allowed). The internet in the resort was patchy, so luckily the goal of the retreat was not to work on anything requiring an internet connection.

People gave a broad outline of what they are doing, followed by one or two things we’re excited about (enables X and Y, or Z is an opportunity), then 5 minutes of questions.

* Camille Scott / Streaming the RNAseq
* Luiz Irber / Architecture of all the buzzwords (amazing basic-level explanation of the internet for those of us who are unfamiliar)
* Taylor Reiter / sourmash RNAseq
* Daniel Standage / kevlar
* Harriet Alexander and Lisa Cohen / MMETSP and challenges of multi-species data analysis
* Tamer Mansour / Progress and opportunities in vet genetics

Sat afternoon, free time!

Weather was great, sunny! We had anticipated not-so-great weather with just-above-freezing rain. But, this was not the case. In the afternoon, we all piled into cars for exploration of Yosemite National Park! Shannon Joslin did an amazing job of summarizing available social activities into this list:

https://docs.google.com/spreadsheets/d/1l7wSBWgvPtG3CqQE6kbWfMnWCt8Ny5cdsounAO7m4v8/edit?pli=1#gid=0

Sat evening, social time!

Jessica Mizzi, who takes fun VERY seriously, coordinated games and activities:

https://docs.google.com/spreadsheets/d/1aecga_zFg6qAlXVql_S11SgaJoi2Ohn-JUok7MPBZ0E/edit#gid=0 

I participated in a few heated games of Settlers of Catan and Pictionary. It turns out there are several members of our lab who are relentless resource emperors and that there are varying degrees of artistic abilities. 🙂

pictionary image-uploaded-from-ios-1
Photos by Camille Scott (left) and Daniel Standage (right)

Sunday morning

Two postdoc lab members recently attended the Moore DDD early career workshop and brought back suggestions for continued discussion on the field of ‘data science’. We found it useful to discuss the larger context of how we market ourselves, develop our careers, and fit ourselves into biological research. Data-intensive biology is a large field. In our lab alone, we represent diverse disciplines, e.g. Software Engineering, Genomics, Biological Oceanography, Comparative Physiology, Medicine, Mathematics, just to name a few. We cannot each have a deep understanding of all of these peripherally-related topics. Yet, our collective knowledge is great. How can we better extract overlapping skills from each other to solve hard problems?

We broke out into 3 groups of 6 people at a mixture of career levels, e.g. beginning grad student, mid-level grad students, postdocs, post-PhD industry-bound to address these specific questions:

* How does Person x learn y topic?
* What works?
* How do we teach Davis community about y topics? (Especially if when we might not necessarily know these things ourselves.)

Discussion points

The following is an approach I’m trying based on some helpful blogging advice: choosing words and phrases explaining what has worked for us (or me, specifically) rather than telling people who read this what they should be doing. This is because I am more apt to listen to someone else’s wisdom gained from their own experiences.

– Learning topics has depended on why we want to learn.

– Up to the learner for finding motivation, not necessarily a list of what others think you need to know. Although, we acknowledged that it is hard to figure out what you need to know, if you don’t know. Some base level knowledge is required.

– We have been told that skills in bioinformatics are required for successful future careers. However, there is no institutional-level plans for how to disseminate these skills to learners.

– Beginning learners can feel overwhelmed because of the interdisciplinary nature of bioinformatics, sometimes requiring a combination of knowledge and skills in computer programming, statistics, cell and molecular biology, etc.

– It has helped many of us to take a project-based learning approach.

– Three motivating scenarios were identified for developing a working knowledge of bioinformatics skills:

  1. Biologist generating data, e.g. RNAseq for differential expression. In the long-term it doesn’t seem to make sense to rely on a sequencing facility to analyze data because decisions made during analysis affect the results. Making these decisions requires revisiting the question of why the data were generated in the first place, which is not necessarily within the scope of an independently contracted analyst to be familiar with. It has been our experience that data are best analyzed by people who know the projects very well.
  2. Data analyst understanding many projects simultaneously and advising those generating and analyzing their own data what is the best way to approach analysis based on their own experiences, consensus in the field and benchmark testing.
  3. Data Scientist at a senior level guiding the direction of a research, training program, and developing new methods for processing data.

– Our lab has representation from all three of these categories.

– Some combination of internet-learning, buddy system, participating in a community are all key aspects of learning bioinformatics skills that seem to work for all of us.

– Buddy system. Many of us have found that forming connections with a person or a community of people at a knowledgeable level to answer questions has been necessary for our learning process. Community and personal connections can be fostered via workshops, classes conferences, social events, friendships.

– We have found good luck with using opportunities to collaborate, asking for advice from experts when we meet them. The great thing about this lab and knowing Titus is being able to take advantage of his far-reaching network of collaborators.

– Internet-learning by Google searching. Stackoverflow is our friend

– Some of us have chosen a good book, e.g. Practical Computing for Biologists by Haddock and Dunn, to read and go through the exercises on a regular basis together with a group of people

– We’ve found it helpful to join a community to ask/answer questions. We are actively working towards fostering such a community at UC Davis via the DIB lab! See our website for training workshop schedule and to sign-up for the email list: http://dib-training.readthedocs.io/en/pub/

– It has been our experience that significant investment of personal time is required to learn.

Here are our flip chart notes from this discussion:

20170205_193406_32618082941_o 20170205_193411_32701005166_o 20170205_193416_31927578523_o

Sunday afternoon

The last afternoon discussion centered around lab culture hacking, i.e. what are we doing well, what needs improvement. A motivational speech from Titus: there are always going to be various things the lab can do better, but generally, we’re in a good place! The lab is a set of opportunities. Choose your own adventure. If we’re not doing something, we can provide resources to accomplish goals. Overall, his expectations are for us to us do wonderful and unexpected things. Preferably multiple wonderful things!

Then Titus left for an hour and a half while we discussed the lab. Topics included more frequent journal club, more frequent project reporting and scrum at every lab meeting (rather than one designated presenter each meeting only presenting slides on their own research the whole time), lab communication on Slack vs. email vs. Google calendar for scheduling. The common theme was that while our projects are all very different, we are all connected and the onus is on us to take more initiative to communicate with one another. We talked about positive and negative aspects of the lab. But generally concluded that our lab is awesome, because of our strong community and diverse backgrounds of our lab members. The meeting adjourned, with some of us returning to watch the Super Bowl while others of us stayed on to play more Settlers of Catan and Pictionary!

Thank you to Yosemite Bug, for the quiet, cozy, accommodating place for our group to stay and be productive this weekend. It was a perfect, small venue for this retreat.

Thank you, Titus for bringing us on this retreat. Thank you, everyone in the DIB lab for being fun people. And thank you, Moore Foundation for funding!

img_8714
Photo by James Word

yosemitebug
Photo by Shannon Joslin






















Read the whole story
luizirber
17 days ago
reply
Lab retreat at Yosemite!
Davis, CA
Share this story
Delete
Next Page of Stories