How to install and update packages in R

A brief tutorial on how to install and update packages in R

Bioinformatics Android Application - GenomeSearch

GenomeSearch is the first Android application that Edwards' Lab has developed. It is a simple Bioinformatics Search which queries theSEED.org for a genome and keyword, and returns search results with links to reference material. Note that in this video, the mouse cursor simulates what a users touch would do on a real phone.

For more information about Dr. Rob Edwards' Lab and projects our team is currently working on, please visithttp://edwards.sdsu.edu/labsite/index...

Bioinformatics : eIUS e-Infrastructure Case Study

The eIUS Project highlights the successful use of e-Infrastructure, in this case by researchers in Bioinformatics at the University of Manchester who, in collaboration with the myGrid Consortium, use the Taverna Workbench and the myExperiment virtual research environment to assist with the analysis and sharing of data relating to sleeping sickness (Trypanosomiasis) in African cattle. The eIUS Project is funded by the JISC and supported by the University of Oxford and University of Manchester.

Translational Bioinformatics: Transforming 300 Billion Points of Data

There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations haven't been well described. The nascent field of translational bioinformatics may help. Dr. Butte's lab at Stanford University builds and applies tools that convert more than 300 billion points of molecular, clinical, and epidemiological data (measured by researchers and clinicians over the past decade) into diagnostics, therapeutics, and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab's work on using publicly available molecular measurements to find new uses for drugs, discovering new treatable mechanisms of disease in type 2 diabetes, and evaluating patients presenting with whole genomes sequenced. 

The NIH Wednesday Afternoon Lecture Series includes weekly scientific talks by some of the top researchers in the biomedical sciences worldwide. 

What is Bioinformatics and Computational Biology?

Bioinformatics Career Overview

A brief overview of Bioinformatics career opportunities brought to you by the University of South Dakota Computer Science Department

Python For Bioinformatics

Were going to go over calculating GC content and making your first Python Program, So if you're a little more advanced and you already know how to use Python, but you'd like to learn more, go ahead and click the link below where I'll show you advanced techniques in learning python for bioinformatics. 

The first thing we're going to need is some data. If you don't have any data, you can't do any bioinformatics, but the great thing is, is there is a ton of free data online ready to go. 

So go ahead and open up your web browser and lets get started, I use chrome. 

Go ahead and type in the Letters NCBI. In the search bar go ahead and type in BRCA 1

Click on this little tab right here that says nucleotide. Up at the top we've got a few things, go ahead and click on the homo sapiens BRCA1, FASTA tab. 

Click on Send in the top right hand corner, click on send to file, and download as FASTA. Then copy that sequence.fasta to a new folder we'll be working in. Replace the name to BRCA1_BAP1.TXT, then you can open it and look at it

Postdoctoral Researcher @ University of Maryland-College Park

Description

A Faculty Research Assistant position is available in a newly established

statistical/quantitative genetics group in the Department of Animal and

Avian Sciences at the University of Maryland, College Park

(http://ansc.umd.edu). Ultimately, the group seeks to understand the genetic

basis of complex traits and diseases, shaped by selection, mutation, and

genetic drift, using statistical and computational approaches. In

particular, the group focuses on developing statistical approaches and

computing tools for the identification of genetic variants for complex

traits and diseases in animals and humans. Detecting selective sweeps and

studying the population history of animals and humans using whole genome

sequence data will also be of interest.

Candidates should have a Ph.D. in genetics, statistics, bioinformatics,

computational biology, computer science, or a related field. Knowledge of

statistical genetics, population genetics, complex trait mapping and/or

next-generation sequencing is a plus. Proficiency in programming in R and

one from Fortran, C/C++, and Java is highly desired. Preference will be

given to candidates with a strong publication record, evidence of

substantial research productivity, and ability to successfully communicate

scientific information.

Salary is highly competitive and commensurate with qualifications. Fringe

benefits are offered.

Applicants can ask for more information through email, lima@umd.edu, or

apply officially through eTerp at https://ejobs.umd.edu, with the position

number 119407. Candidates should upload CV and cover letter with a brief

description of previous research experience and contact information of

three professional references.

• WEBSITE: http://www.umd.edu
• DEPT SITE: http://ansc.umd.edu/faculty/Ma/

Postdoc Researcher @ The Quantitative Biomedical Research Center

Description

The Quantitative Biomedical Research Center is newly established at UT Southwestern Medical Center (UTSW). It aims to foster collaborations involving quantitative methods and technologies in any aspect of biomedical research, particularly for understanding disease etiologies and developing treatment and prevention strategies. Currently, the center has four faculty members, several staff members, postdocs and student research assistants. We are actively recruiting new members to join this new and dynamic group.

Position Title: Postdoctoral Fellow

Duties & Responsibilities: The new postdoc will work on one or more of several interesting topics, including: developing comprehensive predictive models for clinical outcomes, integrated analysis of genetic, genomic and epigenetic data, developing clinical databases. At UTSW, there are many opportunities for postdocs to collaborate with outstanding biomedical investigators and work on exciting research projects. UT Southwestern provides a dynamic, collaborative, and integrative research and training environment with state-of-the-art facilities.

Position Qualifications: Candidates should have a doctoral degree in biostatistics, computer sciences, bioinformatics, electrical engineering, physics or a related field.

ContactEmail: Yang.Xie@UTSouthwestern.edu

Application Deadline: until filled

 UT Southwestern is an Equal Opportunity, Affirmative Action Employer

To apply

Application Address: Dr. Yang Xie (Yang.Xie@ UTSouthwestern.edu) 

WEBSITE: http://www.utsouthwestern.edu

DEPT SITE: http://qbrc.swmed.edu

Post-doctoral Fellow in Neurogenomics @ Brkanac laboratory

Description

The Brkanac laboratory invites applications from highly motivated candidates for a postdoctoral position. We are interested in a discovery of rare highly penetrant variants responsible for familial forms of complex neuropsychiatric diseases using next generation sequencing and bioinformatics approaches. The applicants must hold a Ph.D. level degree in life sciences or computer science with some relevant research experience in both areas and at least one first-authored publication in a peer-reviewed journal. The position requires programming skills, knowledge of bioinformatics including analysis of next generation sequencing data and experience in molecular genetics/genomics. The successful candidate will be self-motivated, keen to acquire new knowledge and skills and eager to produce scientific publications.

The University of Washington is an excellent environment for training in genomics.

Seattle is a desirable to live, vibrant major metropolitan area. To inquire please send a CV, a statement of research interest including description of experience in genomics and bioinformatics and contact information of three references to zbrkanac@uw.edu.

Requirements:

• Ph.D. computer or life sciences or science with some relevant research experience in both areas and at least one first-authored publication in a peer-reviewed journal.

• Background in bioinformatics, molecular biology and genomics .
• Knowledge of bioinformatics tools and genomics databases (dbSNP, UCSC) including data uploads.

• Previous experience with next generation sequencing or GWAS data.

• Experience using Linux operating systems.

• Experience in Perl, Python programming.

• Strong organizational and record keeping skills to record experiment results and analyze data.
• Effective written communication skills to publish results.

To apply

Please send inquires to zbrkanac@uw.edu.

WEBSITE: http://www.uwpsychiatry.org/ResultsDetail.aspx?EmployeeID=741001332

DEPT SITE: http://www.uwpsychiatry.org/ResultsDetail.aspx?EmployeeID=741001332

OncodriveCLUST:identify genes whose mutations are biased towards a large spatial clustering

Description

OncodriveCLUST is a method aimed to identify genes whose mutations are biased towards a large spatial clustering. This method is designed to exploit the feature that mutations in cancer genes, especially oncogenes, often cluster in particular positions of the protein. We consider this as a sign that mutations in these regions change the function of these proteins in a manner that provides an adaptive advantage to cancer cells and consequently are positively selected during clonal evolution of tumours, and this property can thus be used to nominate novel candidate driver genes.

The method does not assume that the baseline mutation probability is homogeneous across all gene positions but it creates a background model using silent mutations. Coding silent mutations are supposed to be under no positive selection and may reflect the baseline clustering of somatic mutations. Given recent evidences of non-random mutation processes along the genome, the assumption of homogenous mutation probabilities is likely an oversimplication introducing bias in the detection of meaningful events.

How it works

Detailed description is contained in the main manuscript. Briefly, the following steps are performed: first, protein affecting mutations of each gene across a cohort of tumors are evaluated looking for those protein residues having a number of mutations barely expected by chance. Second, these positions are thereafter grouped to form mutation clusters. Third, each cluster is scored with a figure proportional to the percentage of the gene mutations that are enclosed within that cluster and inversely related to its length. The gene clustering score is obtained as the sum of the scores of all clusters (if any) found in that gene. Finally, each gene clustering score is compared with the background model to obtain a significance value. Background model is obtained performing the same steps than above but assessing only coding silent mutations.

How it performs

We have analysed those entries of the COSMIC database annotated as whole gene screen as well as data provided from 4 projects of the Cancer Genome Atlas. We demonstrated that the resulting candidate list of drivers is strongly enriched by known cancer driver genes and particularly oncogenes, supporting the idea that this approach can nominate novel driver candidates. In addition, comparison with methods based on other criteria (namely, functional impact and mutation recurrence across the tumor cohort) demonstrated that the clustering approach identifies known cancer drivers not detected by any of the other two methods, stressing the fact that the combination of methods is beneficial to identify cancer drivers. We conclude that OncodriveCLUST is a method that may be useful to identify cancer drivers through the assessment of the mutation clustering property that may be complementary to other methods aimed to identify genes involved in the disease.

How to install and run it

You will find detailed information on how to install OncodriveCLUST and run some examples at Bitbucket

OncodriveCLUST 0.4 is the version for the submitted paper and can be downloaded from here, and the suplementary datasets that have been analysed from here.

How to cite

If you use OncodriveCLUST, please cite it as Tamborero D, Gonzalez-Perez A and Lopez-Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013; doi: 10.1093/bioinformatics/btt395s

For any comments or feedback, please contact

David Tamborero, PhD

Bioinformatician, Postdoctoral Researcher

Research Unit on Biomedical Informatics - GRIB

Parc de Recerca Biomèdica de Barcelona (PRBB)

david.tamborero@upf.edu

NGS (Next generation Sequencing) Data Analyst @ The Centre for Applied Genomics

TCAG, The Centre for Applied Genomics at The Hospital for Sick Children, is one of the leading genomics centres in the world. The TCAG informatics facility is involved in computationally challenging problems such as de-novo genome assembly, identification of potentially pathologic single nucleotide variants utilizing exome or whole-genome re-sequencing and copy number variant detection. TCAG also supports the Database of Genomic Variants (DGV), the major copy number variation database. The Hospital for Sick Children is one of the leading paediatric health care centres in the world with an international reputation for excellence in health care, research, and teaching.

Responsibilities

We are seeking a highly motivated bioinformatics analyst to run and extend analysis pipelines for human/mammalian NGS (next generation sequencing) data, with a specific focus on variant detection in exome and whole genome resequencing applications.

The position will report directly to the informatics core facility manager and will involve close interactions with other informatics facility members.

Requirements

The candidate will have a M.Sc. or equivalent degree in Bioinformatics, Computational Biology, Computer Science, Biomedical Engineering or related fields. Previous experience with NGS data analysis, solid knowledge of scripting languages (Perl, Python, R or Ruby), SQL and Unix OS are strictly required. Excellent communication and team work skills are also required. Strong preference will be given to Canadian citizens, permanent residents as well as graduates of a Canadian institution eligible for a post-graduation work permit.

Preferences

Previous experience exome/whole genome read alignment and variant detection tools is a plus.

Locale

The work will be conducted at the TCAG/The Hospital for Sick Children, Toronto. Toronto is a major international centre of genomics, proteomics and systems biology research; there will ample opportunity for professional development through research seminars, workshops and research in progress meetings.

Compensation

Salary is commensurate with education and qualifications.

Terms

Fixed-term, 2 year contract, with the possibility of extension. TCAG is strongly committed to provide continuative funding for bioinformatics personnel with a good performance record.

Read more/Apply

Director Administration & Finance @ Montreal Neurological Institute

Position Title: 

Dir Admin & Finance (ADM4A)

Position Summary: 

The Director of Administration and Finance of the MNI (Director) is responsible for the internal operations and administrative leadership of the MNI. The Director reports directly to the Director of the MNI (who is also Executive Director of the The Neuro), while working closely and collaboratively with the Senior Director, Administration and Operations of the Faculty of Medicine. The Director leads all administrative operations, including financial activities, HR, technology, procurement and building operations; provides support and guidance to the team of managerial and administrative staff; and enables the high and rigorous performance of the MNI by ensuring administrative and financial functions are aligned to support the financial health and the growth of the MNI, as well as to respect McGill University’s frame of policies and procedures. The Director enthusiastically embraces the mission of the MNI (and of The Neuro) and is a leader, comfortable in an environment driven by research, teaching, knowledge transfer, commercialization, as well as clinical care. The Director is the key resource person to the Executive Director of The Neuro for all administrative and financial matters and, as such, ensures that proper controls, efficient processes and information systems are in place to sustain and improve the overall performance of the MNI. Fundamental to the success of the MNI, the Director develops and maintains excellent relationships and contributes to creating a true sense of partnership and unquestioned added value with the MNI’s key stakeholders: McGill University’s Faculty of Medicine and Central Administration, the Montreal Neurological Hospital and the MUHC.

Primary Responsibilities: 

The following have been identified as key responsibilities for the Director:

1. Be accountable to The Neuro Director for the operational implementation of the strategic plan and establish sound financial operations, including the preparation of an annual budget;
2. Identify the challenges and opportunities arising as a result of the mandate of the MNI and define sound solutions and plans to address those;
3. Monitor the structure, systems and processes to ensure sustainability and growth, to improve productivity and to optimize operational capacity;
4. Ensure controls are in place to secure rigorous and transparent financial reporting;
5. Work in close and harmonious collaboration with the Faculty of Medicine’s management team as regards all administrative and financial affairs of the MNI;
6. Demonstrate a collaborative, solution-oriented style of management and decision-making, all based on high integrity and strong ethics;
7. Leads daily internal operations in areas of finance, HR, technology, legal, procurement, building maintenance, renovation and stewards capital projects ensuring these functions are aligned to support the strategic focus and growth of The MNI and consequently the success of The Neuro, McGill and the MUHC;
8. Maintain an institutional culture that is collaborative, consultative, efficient and effective;
9. Support the MNI program activities in neuroscience research, research support, teaching, commercialization, bioinformatics and knowledge translation;
10. Work with the senior executive team and researchers to build excellent working relationships with all of the MNI’s partners locally, provincially, nationally and internationally so as to advance the MNI’s mission and resource base;
11. Provide oversight to the Clinical Research Unit, Experimental Therapeutics Program, Neuro Research Ethics Board and the PET / Radio Chemistry Core facilityEstablish collegial and respectful relationships with direct reports to create a true sense of belongingness to the MNI and to McGill University.

Minimum Education & Experience: 

Undergraduate degree

Eight (8) years' related experience

Other Qualifying Skills And/Or Abilities: 

In alignment with the key responsibilities of the role, the ideal candidate possesses the following: 8 to 10 years of supervisory financial management experience, including a good understanding of HR, technology, procurement and space management; Formal accounting designation or equivalent; Knowledge of the province of Quebec’s university milieu, including policies and processes; Strategic and conceptual thinking skills, including the ability to anticipate high-level issues and to position the MNI to take advantage of and respond to these issues. Experience in successfully managing sustainability, change and innovation in a dynamic research and academic health setting; Demonstrated commitment towards rigor, performance measurement and accountability; Superior leadership and problem solving skills; Stature and credibility, to assist in the realization of the MNI’s vision. Capacity to appreciate the complexity of an institution like The Neuro, and to work with a diverse community including a broad range of stakeholders – executive team and researchers of the MNI, Faculty of Medicine’s management, University colleagues, MNI donors, governments, other academic institutions, clinical care centers and private sector entities; Entrepreneurial and innovative style, leads with honesty, integrity and empathy, possess the courage to push the envelope in a constructive way; Fluency in English and French – both spoken and written.

Read more/Apply

Trainee/Animal Technician @ The Wellcome Trust Sangter Institute and the European Bioinformatics Institute (EBI)

Salary range: £13,125 to £21,750 per annum dependent on experience. Closing date: 27th September 2013

We are looking to recruit an enthusiastic and committed part-time Trainee/Animal Technician to work 2 days per week (15 hours) pro rata.  The role is to provide husbandry and welfare care to the animals housed primarily within the Research Support Facility (RSF).  This modern facility provides a dedicated aquatics area, mouse containment and quarantine areas and a barriered area giving provision for the housing and utilisation of model organisms in genetics research.

The role will involve working as part of a dedicated team providing high standards of animal care and assistance to the facility users.  You will assist in providing for the husbandry and welfare of the species housed in the RSF.  You will also participate in maintaining fish and mouse breeding and experimental colonies using IVC technology and providing regulated procedures as appropriate.

Essential Skills

1. The post holder should have previous experience working in an animal facility with IAT Level 2 qualification or equivalent experience.
2. It is essential the post holder has an awareness of A(SP)A and the 3 R's and is able to keep neat and accurate records.
3. They should be effective at communicating upwards and liaising with other departments.

 Ideal Skills

1. Previous experience with fish, frogs and rodents, specifically GA and assisting with regulated procedures is highly desirable.
2. Hold a Home Office Personal Licence or have completed Modules 1-3 Training for rodents, fish and frogs.
3. Familiarity with aquatic systems and Individually Ventilated Cages is preferable.
4. Computer literacy and previous experience of entering data onto electronic databases.
5. Awareness of working to SOP's and knowledge of relevant Health & Safety legislation.

Other information

1. The post holder will work within a team of experienced technicians and be supported by highly experienced Principle Technicians and Managers.  This team will nurture good decision making and promote ownership of activities.
2. There is a requirement to participate in a weekend and public holiday rota (this will involve working approximately 1 weekend in 3) to ensure the RSF is satisfactorily maintained at all times.  The role will also occasionally require hours to be worked outside of the normal hours to fit with RSF User requests.
3. The post holder will be given appropriate training to allow them to fully undertake their role.
4. The work involves some manual lifting and much of the day is spent standing.
5. The Genome Campus is a 55 acre estate south of Cambridge in the grounds of Hinxton Hall.  Nestled in the quiet countryside of these landscaped gardens, are two world class research facilities:  The Wellcome Trust Sangter Institute and the European Bioinformatics Institute (EBI).  The site has become the British hub of biomedical science.  The Campus is also home to the Wellcome Trust Advanced Courses and Scientific Conferences program and the Wellcome Trust Conference Centre.
6. In addition to its peaceful location the campus offers excellent facilities including a state of the art data centre, gym, 2 cafes, nursery, dining facilities, a cycle to work scheme, car sharing and free campus buses from various locations around Cambridge.
7. Equally important to campus life is the range of social activities offered by the Sports and Social Club whether it is a Burns Night Supper, the Mid-Summer Ball or a quiz night.  There are opportunities to meet with people working across the organisation.
8. Learning, development and networking are other important aspects of life on campus.  There are a range of scientific seminars with our own invited speakers, scientific group meetings and skills development workshops.

When applying please submit a CV and a covering letter.

Closing date for applications is 27nd September 2013.

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Proteomics & Bioinformatics Journals OMICS Publishing Group

This video belongs to Proteomics which is the study of proteins expressed by a genome. Bioinformatics is the analysis of biological information using computational and various statistical techniques. The journal provides an Open Access platform by OMICS Publishing Group to publish latest advancements in the field of proteomics and bioinformatics.In Proteomics & Bioinformatics, expert researchers explore this ever-changing field, providing the reader with a mix of review and methodology chapters which address the fundamentals of analysis methods, algorithms, data standards and databases. This supports the journals which publishes original research articles in all areas of experiment and applied proteomics & bioinformatics. In past years Journal of Proteomics & Bioinformatics has been showing tremendous citations and articles focusing the most advanced research trends. 

To access more information about Journal of Proteomics & Bioinformatics please follow OMICS Publishing Group's official page

Onexus:Data analysis life cycle management

Data analysis life cycle

Onexus is a modular framework to manage the complete life cycle of data analyses. Data analyses follow these steps: analysis definition, analysis execution, results storing, results browsing and finally results publishing.

(show details)

Use case

Onexus is a general framework, so its functionality depends on the implemented modules. On the first release we want to focus on making Onexus useful for this use case:

Easily build a website with big datasets

The website will allow your visitors to browse, filter and download data of their interest. Check this sitebeta.intogen.org to see what we are doing with an alpha version of Onexus. You will also get a webservice so your visitors will be able to automatically do downloads from their scripts.

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