LabKey Software

http://medcitynews.com/2014/01/open-sourced-seattle-fated-collision-software-talent-life-science-researchers/#ixzz2rLZYJd7B

LabKey Server is open source software that helps scientists organize, analyze, and share biomedical research data.

Read more: http://medcitynews.com/2014/01/open-sourced-seattle-fated-collision-software-talent-life-science-researchers/#ixzz2rLvIbCgM

https://labkey.org/

The gut–microbiome–brain connection

http://www.nature.com/nrn/journal/v15/n2/full/nrn3669.html?WT.ec_id=NRN-201402

Nature Reviews Neuroscience

 

15,

 

65

 

(2014)

 

doi:10.1038/nrn3669

Published online

 

27 December 2013

 

Studies in mice and human patients suggest that microbial imbalances in the gut influence various social, emotional and anxiety-like behaviours. Interestingly, gastrointestinal (GI) problems are common in autism spectrum disorders (ASDs), which are associated with social interaction deficits and stereotypical behaviours. A new study in Cell provides evidence that alterations in commensal gut bacteria contribute to certain behavioural abnormalities in a mouse model of ASD, highlighting the potential benefit of probiotic therapies for some of the features of such disorders.

1. Hsiao, E. Y. et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cellhttp://dx.doi.org/10.1016/j.cell.2013.11.024 (2013)

The Toxins of William B. Coley and the Treatment of Bone and Soft-Tissue Sarcomas

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1888599/

In 1891, William B. Coley injected streptococcal organisms into a patient with inoperable cancer. He thought that the infection he produced would have the side effect of shrinking the malignant tumor. He was successful, and this was one of the first examples of immunotherapy. Over the next forty years, as head of the Bone Tumor Service at Memorial Hospital in New York, Coley injected more than 1000 cancer patients with bacteria or bacterial products. These products became known as Coley's Toxins. He and other doctors who used them reported excellent results, especially in bone and soft-tissue sarcomas.

Despite his reported good results, Coley's Toxins came under a great deal of criticism because many doctors did not believe his results. This criticism, along with the development of radiation therapy and chemotherapy, caused Coley's Toxins to gradually disappear from use. However, the modern science of immunology has shown that Coley's principles were correct and that some cancers are sensitive to an enhanced immune system. Because research is very active in this field, William B. Coley, a bone sarcoma surgeon, deserves the title "Father of Immunotherapy."

A Field Guide to Genomics Research

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001744

High-throughput technologies are enabling scientists to profile genomes, transcriptomes, proteomes, and metabolomes at an unprecedented scale[1]. All this “-omics” research (let's call it genomics for simplicity) is exciting—and game changing—but it's also fraught with dangers for the tenderfoot. Here, we've put together a brief “field guide” for those wishing to visit the genomics frontier, in which we use caricatures to illustrate various pitfalls that can beset those who inhabit this new territory. By documenting the behaviors of these common types, we hope to guide researchers in their quest to apply sound practices when designing genomics experiments and analyzing the resulting data. Many of the tendencies we have encountered are not specific to genomics research, but they are particularly acute in this field due to its interdisciplinary nature and the complexity of the data it produces.

The Farmer

“Let's harvest a bunch of data and design fancy tools, and then we'll figure out what to do with them.”

...

Scientists tell the truth…

http://themetapicture.com/scientists-tell-the-truth/

What is aging?

https://www.youtube.com/watch?feature=player_embedded&v=jc4yK0zZ-cQ

Making better inferences from statistical graphics Edward Tufte

http://www.edwardtufte.com/bboard/q-and-a-fetch-msg?msg_id=0003wa#!

http://pps.sagepub.com/content/7/6/645.full

Why Science Is Not Necessarily Self-Correcting

The ability to self-correct is considered a hallmark of science. However, self-correction does not always happen to scientific evidence by default

Drug Research in China Falls Under a Cloud

http://www.nytimes.com/2013/07/23/business/global/drug-research-in-china-falls-under-a-cloud.html?hp&_r=0

The report revealed that the drug’s project leader belatedly learned the results of three studies of ozanezumab in mice. During their investigation, auditors came across six studies whose results had not been reported, even though early trials in humans were already under way.

“If that’s true, it’s a mortal sin in research requirements,” said Arthur L. Caplan, the head of the division of medical ethics at NYU Langone Medical Center. He served as the chairman of an advisory committee on bioethics at Glaxo from 2005 to 2008. “No one could approve human trials without having that information available, scientifically or ethically. That’s kind of a Rock-of-Gibraltar-sized ethics violation.”

Best Places to Work Academia, 2012

http://www.the-scientist.com/?articles.view/articleNo/32392/title/Best-Places-to-Work-Academia--2012/

 Sage Bionetworks, Seattle Washington
Center for Molecular Medicine (CeMM) of the Austrian Academy of Sciences 

Government of Canada invests in research-driven knowledge economy

http://www.innovation.ca/en/Media/News/GovernmentCanadainvestsinresearchdrivenknowledgeeconomy#ubc

University of British Columbia (The)

Leading Edge Fund / Fonds de l’avant-garde
Immune System Polymorphism and Host/Pathogen Interactions	$2,104,522
A Digital Radio Telescope for CHIME: Three Dimensional Mapping of the Largest Volume of the Universe to Date	$4,585,372
Envirotron for Plant Adaptation Research	$1,061,030
Genomic Approaches to Personalizing Cancer Diagnosis and Treatment	$5,681,816
Molecules to Human: Enhanced Phenotyping for Discovery, Prevention, and Treatment of Heart, Lung, and Blood Vessel Disease	$2,498,597
Quantum Materials and Devices Foundry	$1,739,738
Super Resolution Microscopy: Breaking the Diffraction Barrier	$1,407,645
Systems Analysis of Single Stem Cells	$2,977,910

http://www.grad.ubc.ca/aggregator

Improbable Research

http://www.improbable.com/ig/winners/#ig2012
http://www.jsur.org/ - Journal of Serendipitous and Unexpected Results

The 2012 Ig Nobel Prize Winners

Winners were announced and awarded on Thursday night, September 20. The ceremony was webcast live. For more information, check the ceremony page.
PSYCHOLOGY PRIZE: Anita Eerland and Rolf Zwaan [THE NETHERLANDS] and Tulio Guadalupe [PERU, RUSSIA, and THE NETHERLANDS] for their study "Leaning to the Left Makes the Eiffel Tower Seem Smaller"
REFERENCE: "Leaning to the Left Makes the Eiffel Tower Seem Smaller: Posture-Modulated Estimation," Anita Eerland, Tulio M. Guadalupe and Rolf A. Zwaan, Psychological Science, vol. 22 no. 12, December 2011, pp. 1511-14.
ATTENDING THE CEREMONY: Tulio Guadalupe. [NOTE: Two days after the ceremony, Anita Eerland and Rolf Zwaan married each other, in the Netherlands.]

PEACE PRIZE: The SKN Company [RUSSIA], for converting old Russian ammunition into new diamonds.
ATTENDING THE CEREMONY: Igor Petrov

ACOUSTICS PRIZE: Kazutaka Kurihara and Koji Tsukada [JAPAN] for creating the SpeechJammer — a machine that disrupts a person's speech, by making them hear their own spoken words at a very slight delay.
REFERENCE: "SpeechJammer: A System Utilizing Artificial Speech Disturbance with Delayed Auditory Feedback", Kazutaka Kurihara, Koji Tsukada, arxiv.org/abs/1202.6106. February 28, 2012.
ATTENDING THE CEREMONY: Kazutaka Kurihara and Koji Tsukada

NEUROSCIENCE PRIZE: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford [USA], for demonstrating that brain researchers, by using complicated instruments and simple statistics, can see meaningful brain activity anywhere — even in a dead salmon.
REFERENCE: "Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction," Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, poster, 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, CA, June 2009.
REFERENCE: "Neural Correlates of Interspecies Perspective Taking in the Post-Mortem Atlantic Salmon: An Argument For Multiple Comparisons Correction," Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, Journal of Serendipitous and Unexpected Results, vol. 1, no. 1, 2010, pp. 1-5.
ATTENDING THE CEREMONY: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford

Collaborations: The rise of research networks

http://www.nature.com/nature/journal/v490/n7420/full/490335a.html?WT.ec_id=NATURE-20121018

• Jonathan Adams

Nature

 

490,

 

335–336

 

(18 October 2012)

 

doi:10.1038/490335a

Published online

 

17 October 2012

New collaboration patterns are changing the global balance of science. Established superpowers need to keep up or be left behind, says Jonathan Adams.

Mendeley is a free reference manager and academic social network

It’s time to change the way we do research.

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

• Automatically generate bibliographies
• Collaborate easily with other researchers online
• Easily import papers from other research software
• Find relevant papers based on what you’re reading
• Access your papers from anywhere online
• Read papers on the go, with our new iPhone app

http://www.mendeley.com/

No shame

The handling of results suggesting faster-than-light neutrinos was a model of fitting behaviour.

Physicists saw plenty of reasons to doubt OPERA's extraordinary claim, and Ereditato and Auterio did not disagree. Even as they presented the result, they invited their colleagues to comment, and encouraged others to try to reproduce their results. Within months, CERN had sent a new beam of neutrinos to Italy and a second experiment found neutrinos travelling at the expected speed. After a great deal of searching, members of the OPERA group eventually traced the discrepancy to a cable that was not fully screwed in.

“The message here is that scientists are not afraid to question the big ideas.”

Ereditato and Auterio acted responsibly when speaking publicly by sticking close to their data and avoiding over-interpretation.

Some Italian journalists aside, the press responsibly reported the initial result as simultaneously incredible and very possibly wrong.

The no-confidence vote and resignations are a matter for the collaboration's internal processes, and have no bearing on the quality of the collaboration's science.

http://www.nature.com/nature/journal/v484/n7394/full/484287b.html?WT.ec_id=NATURE-20120419

Blue sky science

Blue skies research (also called blue sky science) is scientific research in domains where "real-world" applications are not immediately apparent. It has been defined as "research without a clear goal"^[1] and "curiosity-driven science." It is sometimes used interchangeably with the term "basic research."^[2]

http://en.wikipedia.org/wiki/Blue_skies_research

Privacy Best Practices - Ethics

• PBP 2005 http://cihr-irsc.gc.ca/e/22085.html
• PBPs Initial Implementation Phase 2005-2007 http://cihr-irsc.gc.ca/e/29138.html