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http://ittakes30.wordpress.com/

Blog about the interests of the Department of Systems Biology at Harvard Medical School. They use tools from physics, mathematics and computer science to help us better understand the behavior of biological systems, large and small. Jobs and postdoc positions are available under the corresponding categories. Interests: * Methods for quantitative measurement, and for data analysis. Although much is said about the flood of new data in biology, nearly every time you want to understand a biological system at a mathematical or mechanical level you find that the numbers you need most are missing. Measuring and extracting the parameters that describe key features of the system is a major interest. * Theoretical and computational methods that can cope with the special features of biological systems. Issues such as combinatorial complexity, stochasticity, and variation from individual to individual and tissue to tissue are hard to deal with using conventional tools. * Philosophies of modeling. How do we represent what we know about the system what level of abstraction is appropriate for a given question, what is important and what can be ignored? What are models useful for? * Evolution. One of the more useful tools to identify what''s important is evolution a comparison across species helps to show what is allowed to change and what is not. * Synthetic biology. If I understand it, can I build it? (And in any case, can I build useful stuff?) They will post thoughts about recent papers in the literature that they find interesting, news about the Department, and information about Department Alumni. Please check back frequently, and feel free to comment.

Proper citation: It Takes 30 (RRID:SCR_006882) Copy   

•   Source: SciCrunch Registry
  

http://physionet.org/physiobank/

Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them.

Proper citation: Physiobank (RRID:SCR_006949) Copy   

•   Source: SciCrunch Registry
  

http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry
  

https://cgc.umn.edu

Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available.

Proper citation: Caenorhabditis Genetics Center (RRID:SCR_007341) Copy   

•   Source: SciCrunch Registry
  

https://ranchobiosciences.com/

Company offers Data Curation, Data Governance and Models, Bioinformatics Analysis, Workflows and Pipelines, Knowledge Mining, Target Profiles, Building Databases with content, Business Analyst services to clients in Pharmaceutical and Biotech companies, Foundations, Government and Hospitals.

Proper citation: RanchoBiosciences (RRID:SCR_007252) Copy   

•   Source: SciCrunch Registry
  

http://senselab.med.yale.edu/ordb/

Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors.

Proper citation: Olfactory Receptor DataBase (RRID:SCR_007830) Copy   

•   Source: SciCrunch Registry
  

http://www.cellml.org/models

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

Proper citation: CellML Model Repository (RRID:SCR_008113) Copy   

•   Source: SciCrunch Registry
  

http://www.biocompare.com/

A web catalog of over 1M antibodies from hundreds of different companies and other research supplies. Biocompare has made large quantities of data available to the antibodyregistry.org facilitating tagging important research reagents to literature and continues to work with the antibodyregistry.

Proper citation: Biocompare (RRID:SCR_008336) Copy   

•   Source: SciCrunch Registry
  

http://www.jurgott.org/linkage/ListSoftware.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.

Proper citation: Genetic Analysis Software (RRID:SCR_013155) Copy   

•   Source: SciCrunch Registry
  

http://roadmapepigenomics.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data.

Proper citation: Roadmap Epigenomics Project (RRID:SCR_008924) Copy   

•   Source: SciCrunch Registry
  

http://www.nature.com/nature/podcast/index.html

A weekly podcast which features highlighted content from the week''s edition of Nature including interviews with the people behind the science, and in-depth commentary and analysis from journalists covering science around the world.

Proper citation: Nature Podcast (RRID:SCR_010552) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/scicrunch/data/source/nlx_154697-11/search?q=*

A virtual database indexing video and other multimedia content from: NIH VideoCasting and Podcasting, JoVE: Journal of Visualized Experiments, The Guardian: Science Videos, Biointeractive, goCognitive, UCSF Laboratory for Visual Neuroscience, and Clarity resources.

Proper citation: Integrated Videos (RRID:SCR_003613) Copy   

•   Source: SciCrunch Registry
  

http://blogs.scientificamerican.com/cross-check/

Every week, John Horgan takes a puckish, provocative look at breaking science. A former staff writer at Scientific American, he is the author of four books, the most recent of which is The End of War (to be published by McSweeney''s Books January 17, 2012). He currently directs the Center for Science Writings at Stevens Institute of Technology. He lives in New York State''s Hudson Highlands, where he plays ice hockey each winter to hone his cross-checking skills.

Proper citation: Scientific American Cross-Check (RRID:SCR_004266) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/scicrunch/data/source/nlx_154697-10/search?q=*&l=

A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).

Proper citation: Integrated Software (RRID:SCR_004745) Copy   

•   Source: SciCrunch Registry
  

http://scienceblogs.com/channel/life-science/

ScienceBlogs posts about Life Science.

Proper citation: ScienceBlogs: Life Science (RRID:SCR_005158) Copy   

•   Source: SciCrunch Registry
  

http://blogs.scientificamerican.com/guest-blog/

The editors of Scientific American regularly encounter perspectives on science and technology that we believe our readers would find thought-provoking, fascinating, debatable and challenging. The guest blog is a forum for such opinions. The views expressed belong to the author and are not necessarily shared by Scientific American.

Proper citation: Scientific American Guest Blog (RRID:SCR_005152) Copy   

•   Source: SciCrunch Registry
  

http://www.scientificamerican.com/section.cfm?id=bering-in-mind

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Science news and technology updates from Scientific American.

Proper citation: Scientific American Bering in Mind (RRID:SCR_005208) Copy   

•   Source: SciCrunch Registry
  

http://network.nature.com/blogs

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25,2022.NOTE:Blogs hosted on Nature Network have now moved to new homes in the Nature Publishing Group network of blogs. We''''ve made these changes so that our bloggers can take advantage of improvements in blogging technology, and so that we can offer a better service to our colleagues and those who choose to blog with us. We are no longer hosting blogs on Nature Network itself. Nature Network Blogs are blogs posted by members of Nature Network, the professional networking website for scientists around the world. All features on Nature Network are completely free. All you need to do is create a profile.

Proper citation: Nature Network Blogs (RRID:SCR_005165) Copy   

•   Source: SciCrunch Registry
  

https://rrid.site/rin/sources/SCR_005400

SciCrunch Registry, formerly NIF Registry, provides biomedical resources catalog. Each resource obtains RRID (Research Resource Identifier) upon registration. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.

Proper citation: SciCrunch Registry (RRID:SCR_005400) Copy   

•   Source: SciCrunch Registry
  

http://blogs.discovermagazine.com/neuroskeptic/

A blog by a neuroscientist (United Kingdom) that takes a skeptical look at his own field, and beyond.

Proper citation: Neuroskeptic (RRID:SCR_005427) Copy   

•   Source: SciCrunch Registry