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Tuesday, January 3, 2012
The Gaggle: an open-source software system for integrating bioinformatics software and data sources.
http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Search&doptcmdl=Citation&defaultField=Title%20Word&term=Shannon[author]%20AND%20The%20Gaggle%3A%20an%20open-source%20software%20system%20for%20integrating%20bioinformatics%20software%20and%20data%20sources.
Abstract
BACKGROUND:
Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing.
RESULTS:
In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools.
CONCLUSION:
We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at http://gaggle.systemsbiology.net.
Abstract
BACKGROUND:
Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity of systems biology data sets. A solution to this problem should recognize that data types, formats and software in this high throughput age of biology are constantly changing.
RESULTS:
In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration. Guided by the classic software engineering strategy of separation of concerns and a policy of semantic flexibility, it integrates existing popular programs and web resources into a user-friendly, easily-extended environment. We demonstrate that four simple data types (names, matrices, networks, and associative arrays) are sufficient to bring together diverse databases and software. We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous data exploration using a wide range of publicly available data and a variety of popular bioinformatics software tools.
CONCLUSION:
We have integrated diverse databases (for example, KEGG, BioCyc, String) and software (Cytoscape, DataMatrixViewer, R statistical environment, and TIGR Microarray Expression Viewer). Through this loose coupling of diverse software and databases the Gaggle enables simultaneous exploration of experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon, chromosomal proximity, phylogenetic pattern), metabolic pathways (KEGG) and Pubmed abstracts (STRING web resource), creating an exploratory environment useful to 'web browser and spreadsheet biologists', to statistically savvy computational biologists, and those in between. The Gaggle uses Java RMI and Java Web Start technologies and can be found at http://gaggle.systemsbiology.net.
Rare diseases
http://www.socialstyrelsen.se/rarediseases
In the database for rare diseases of the Swedish National Board of Health and Welfare you can find information about diseases or disorders which affect fewer than 100 people per million, and which lead to a marked degree of disability.
In the database for rare diseases of the Swedish National Board of Health and Welfare you can find information about diseases or disorders which affect fewer than 100 people per million, and which lead to a marked degree of disability.
Human genetics: Genomes on prescription
http://www.nature.com/news/2011/111005/full/478022a.html
As prices fall further, some say that prescribing a genome sequence or analysis will become akin to requesting a magnetic resonance imaging (MRI) scan. "It's just like any other test in medicine. There's nothing remotely special about it," says David Bick, a clinical geneticist at the Medical College of Wisconsin in Milwaukee. But, he adds, "people will cry and scream and yell about that statement". That's true: unlike the results of most medical tests, a genome sequence provides a vast amount of difficult-to-interpret data, not all of which will be necessary for diagnosing or treating the patient's condition and which could provide unwanted clues to future health risks.
they identified a mutation on the X chromosome in a gene called X-linked inhibitor of Apoptosis, or XIAP (ref. 3). A deficiency of the protein encoded by this gene is known to put patients at high risk for a deadly immune-cell disorder,
http://www.nature.com/news/2011/111005/full/478022a.html#B3
As prices fall further, some say that prescribing a genome sequence or analysis will become akin to requesting a magnetic resonance imaging (MRI) scan. "It's just like any other test in medicine. There's nothing remotely special about it," says David Bick, a clinical geneticist at the Medical College of Wisconsin in Milwaukee. But, he adds, "people will cry and scream and yell about that statement". That's true: unlike the results of most medical tests, a genome sequence provides a vast amount of difficult-to-interpret data, not all of which will be necessary for diagnosing or treating the patient's condition and which could provide unwanted clues to future health risks.
they identified a mutation on the X chromosome in a gene called X-linked inhibitor of Apoptosis, or XIAP (ref. 3). A deficiency of the protein encoded by this gene is known to put patients at high risk for a deadly immune-cell disorder,
http://www.nature.com/news/2011/111005/full/478022a.html#B3
Cell signalling caught in the act
http://www.nature.com/news/2011/110719/full/475273a.html
The structure of this complex could finally reveal how one of biology's most important signalling mechanisms, G-protein-coupled receptors (GPCRs), do their job. This structure, published online in Nature1 by a team led by Kobilka at Stanford University in California and Roger Sunahara at the University of Michigan in Ann Arbor, now reveals the complete three-dimensional atomic structure of an activated GPCR — the β2 adrenergic receptor (β2AR) — in a complex with its G protein.
GPCRs sit in the membranes of cells throughout the body, where they detect signals from the outside world — such as light, odours and flavours — and signals from within the body, such as hormones and neurotransmitters. These signals are transmitted to the inside of the cell where they activate intracellular G proteins, which then trigger a variety of biochemical pathways.
The β2AR is activated by the hormones adrenaline and noradrenaline, and kicks off the body's fight-or-flight response by speeding up the heart and opening airways. It is a key target for anti-asthma drugs. Kobilka's X-ray crystallographic snapshot of β2AR associated with its G protein reveals some surprises, and could help in the design of more effective medicines — GPCRs are targeted by between one-third and one-half of all drugs on the market, including most of the best-sellers.
The structure of this complex could finally reveal how one of biology's most important signalling mechanisms, G-protein-coupled receptors (GPCRs), do their job. This structure, published online in Nature1 by a team led by Kobilka at Stanford University in California and Roger Sunahara at the University of Michigan in Ann Arbor, now reveals the complete three-dimensional atomic structure of an activated GPCR — the β2 adrenergic receptor (β2AR) — in a complex with its G protein.
GPCRs sit in the membranes of cells throughout the body, where they detect signals from the outside world — such as light, odours and flavours — and signals from within the body, such as hormones and neurotransmitters. These signals are transmitted to the inside of the cell where they activate intracellular G proteins, which then trigger a variety of biochemical pathways.
The β2AR is activated by the hormones adrenaline and noradrenaline, and kicks off the body's fight-or-flight response by speeding up the heart and opening airways. It is a key target for anti-asthma drugs. Kobilka's X-ray crystallographic snapshot of β2AR associated with its G protein reveals some surprises, and could help in the design of more effective medicines — GPCRs are targeted by between one-third and one-half of all drugs on the market, including most of the best-sellers.
communicating your work is essential
"However, the best advice I can
probably give you is that if you feel the reviewers didn't understand your
work, it is most likely because you didn't explain it as well as you
should. If you feel the reviewers did not understand the significance or
coolness of your work, it is most likely because you failed to communicate
it. The one big lesson I hope you get from this is that communicating your
work is essential. People with good communication skills have a far higher
chance of succeeding in industry, business and/or academia. " --
Nando, cpsc540
probably give you is that if you feel the reviewers didn't understand your
work, it is most likely because you didn't explain it as well as you
should. If you feel the reviewers did not understand the significance or
coolness of your work, it is most likely because you failed to communicate
it. The one big lesson I hope you get from this is that communicating your
work is essential. People with good communication skills have a far higher
chance of succeeding in industry, business and/or academia. " --
Nando, cpsc540
Flexible, foldable, actively multiplexed, high-density electrode array for mapping brain activity in vivo
http://www.nature.com/neuro/journal/v14/n12/full/nn.2973.html
Arrays of electrodes for recording and stimulating the brain are used throughout clinical medicine and basic neuroscience research, yet are unable to sample large areas of the brain while maintaining high spatial resolution because of the need to individually wire each passive sensor at the electrode-tissue interface. To overcome this constraint, we developed new devices that integrate ultrathin and flexible silicon nanomembrane transistors into the electrode array, enabling new dense arrays of thousands of amplified and multiplexed sensors that are connected using fewer wires. We used this system to record spatial properties of cat brain activity in vivo, including sleep spindles, single-trial visual evoked responses and electrographic seizures. We found that seizures may manifest as recurrent spiral waves that propagate in the neocortex. The developments reported here herald a new generation of diagnostic and therapeutic brain-machine interface devices.
Arrays of electrodes for recording and stimulating the brain are used throughout clinical medicine and basic neuroscience research, yet are unable to sample large areas of the brain while maintaining high spatial resolution because of the need to individually wire each passive sensor at the electrode-tissue interface. To overcome this constraint, we developed new devices that integrate ultrathin and flexible silicon nanomembrane transistors into the electrode array, enabling new dense arrays of thousands of amplified and multiplexed sensors that are connected using fewer wires. We used this system to record spatial properties of cat brain activity in vivo, including sleep spindles, single-trial visual evoked responses and electrographic seizures. We found that seizures may manifest as recurrent spiral waves that propagate in the neocortex. The developments reported here herald a new generation of diagnostic and therapeutic brain-machine interface devices.
Democrat vs Republican
http://www.diffen.com/difference/Democrat_vs_Republican
Obama is a democrat (social)
Bush is a republican (individual, corporate)
Differences in Philosophy
While there may be several differences in opinion between individual Democrats and Republicans on certain issues, what follows is a generalization of their stand on several of these issues. A Democrat is typically known as a supporter of a broader range of social services in America than those advocated by Republicans. Republican philosophy is based on a limited influence of government and a dominant foreign policy.
Republicans are considered on the "right" end of the political spectrum while Democrats are on the "left." The far right generally is pro-religion, anti-bureaucracy, pro-military, pro-business and pro-personal responsibility.
Republicans, are usually considered conservative (fiscally as well as socially), maybe a little pious, pro-business and against the bureaucracy often associated with big government. They see big governments as wasteful and an obstacle to getting things done. Their approach is Darwinian in that the strong shall survive, cream rises to the top, etc.
To the far left of the spectrum are the extreme liberal, or the most extreme democrats. Democrats are considered more liberal. Democrats tend to favor an active role for government in society and believe that such involvement – be it environmental regulations against polluting or anti-discrimination laws – can improve the quality of people’s lives and help achieve the larger goals of opportunity and equality. On the other hand, Republicans tend to favor a limited role for government in society and believe that such reliance on the private sector (businesses and individuals) – be it avoiding unnecessary environmental regulations or heavy-handed anti-discrimination laws – can improve economic productivity and help achieve the larger goals of freedom and self-reliance
Obama is a democrat (social)
Bush is a republican (individual, corporate)
Differences in Philosophy
While there may be several differences in opinion between individual Democrats and Republicans on certain issues, what follows is a generalization of their stand on several of these issues. A Democrat is typically known as a supporter of a broader range of social services in America than those advocated by Republicans. Republican philosophy is based on a limited influence of government and a dominant foreign policy.
Republicans are considered on the "right" end of the political spectrum while Democrats are on the "left." The far right generally is pro-religion, anti-bureaucracy, pro-military, pro-business and pro-personal responsibility.
Republicans, are usually considered conservative (fiscally as well as socially), maybe a little pious, pro-business and against the bureaucracy often associated with big government. They see big governments as wasteful and an obstacle to getting things done. Their approach is Darwinian in that the strong shall survive, cream rises to the top, etc.
To the far left of the spectrum are the extreme liberal, or the most extreme democrats. Democrats are considered more liberal. Democrats tend to favor an active role for government in society and believe that such involvement – be it environmental regulations against polluting or anti-discrimination laws – can improve the quality of people’s lives and help achieve the larger goals of opportunity and equality. On the other hand, Republicans tend to favor a limited role for government in society and believe that such reliance on the private sector (businesses and individuals) – be it avoiding unnecessary environmental regulations or heavy-handed anti-discrimination laws – can improve economic productivity and help achieve the larger goals of freedom and self-reliance
365 days: Nature's 10 - Ten people who mattered this year.
http://www.nature.com/news/365-days-nature-s-10-1.9678
Dario Autiero: Relativity challenger
Sara Seager: Planet seeker
Lisa Jackson: Pollution cop
Essam Sharaf: Science revolutionary
Diederik Stapel: Fallen star (fraudulent research, a psychologist from Tilburg University in the Netherlands) (as well as Marc Hauser, Harvard, evolutionary psychologist)
Rosie Redfield: Critical enquirer (Canadian microbiologist) "a propensity to say what was on her mind"
Danica May Comacho: Child of the times (7-billionth baby) in the Philippines
Mike Lamont: The Higgs mechanic
Tatsuhiko Kodama: Fukushima's gadfly (gadfly: a fly that annoys horses and other livestock)
John Rogers: Tech exec
Dario Autiero: Relativity challenger
Sara Seager: Planet seeker
Lisa Jackson: Pollution cop
Essam Sharaf: Science revolutionary
Diederik Stapel: Fallen star (fraudulent research, a psychologist from Tilburg University in the Netherlands) (as well as Marc Hauser, Harvard, evolutionary psychologist)
Rosie Redfield: Critical enquirer (Canadian microbiologist) "a propensity to say what was on her mind"
Danica May Comacho: Child of the times (7-billionth baby) in the Philippines
Mike Lamont: The Higgs mechanic
Tatsuhiko Kodama: Fukushima's gadfly (gadfly: a fly that annoys horses and other livestock)
John Rogers: Tech exec
perseverance
"You've got to say, I think that if I keep working at this and want it badly enough I can have it. It's called perseverance."
Functional Genomics Laboratory: Gingeras Group
http://gingeraslab.cshl.edu/
Expression and Proliferation Program. We are located in the Genome Center on the Woodbury campus. Our laboratory employs empirical and computational approaches to study the organization of information found within genomes and the roles non-protein coding RNAs assume both as part of the informational content and regulation of the protein coding content. Central to these studies is the analysis of the transcriptional content expressed by cells (transcriptomes) and the epigenetic marks found on both genomes and chromatin that influence the expression levels and timing of transcriptomes. These studies require whole genome analyses using high density microarray and deep nucleotide sequencing. The generation of such very large sets has prompted us to develop and to utilize novel computational tools: to store, to analyze, to curate, to graphically display and to make these data sets available for the scientific community.
Expression and Proliferation Program. We are located in the Genome Center on the Woodbury campus. Our laboratory employs empirical and computational approaches to study the organization of information found within genomes and the roles non-protein coding RNAs assume both as part of the informational content and regulation of the protein coding content. Central to these studies is the analysis of the transcriptional content expressed by cells (transcriptomes) and the epigenetic marks found on both genomes and chromatin that influence the expression levels and timing of transcriptomes. These studies require whole genome analyses using high density microarray and deep nucleotide sequencing. The generation of such very large sets has prompted us to develop and to utilize novel computational tools: to store, to analyze, to curate, to graphically display and to make these data sets available for the scientific community.
Electrical 'deep brain' depression treatment safe, effective: Research
An experimental treatment first performed in Canada that uses electrical currents to reset the brain can ease the torment of treatment-resistant depression for at least two years, new research suggests.
http://www.vancouversun.com/health/Electrical+deep+brain+depression+treatment+safe+effective+Research/5936610/story.html
http://www.vancouversun.com/health/Electrical+deep+brain+depression+treatment+safe+effective+Research/5936610/story.html
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