Can We Use Modern Science Efficiently in time to save Earth?
Yes.. and using THIS tool is the answer. BUT we need lots of people to use it and network on harvesting the best solutions available on a global scale. Think of it as the Wikipedia of the Medical Field. Matter of fact. Combine it. Remove all possible profiteering opportunities. Legislate against monopoly on a bigger scale. Charge real criminals, don’t circumvent with abuse, that should be dishonorably frowned upon by real honorable Judges. We should begin forced resignations of Judges against Cannabis. And all Gov employees against it.. this is at the importance level with domestic violence and hate crimes whether racism or homophobia crimes.
Next.. cigarettes/tobacco, big pharma and Alcohol
Upload and graphically compare your own data with NCBI Epigenomics tracks
Wednesday, June 26, 2013
The NCBI Epigenomics resource, a comprehensive public repository for whole-genome epigenetic datasets, contains information from a subset of data in the Gene Expression Omnibus (GEO), which has been subjected to additional review and annotation. Currently there are over 4200 viewable and downloadable datasets from over 1200 samples that have been isolated from five well-studied species.
From the NCBI Epigenomics homepage (Figure 1A), you can access the “Upload” page where your own datasets can be uploaded and displayed as tracks in the Epigenomics genome viewer.
Please note that the “Upload Tracks” feature requires logging into a My NCBI Account which facilitates the storing of information for future examination and also ensures that the data is only visible and viewable by the account holder. The uploaded information cannot be viewed, downloaded or used by any other user of the Epigenomics resource.
Once logged into NCBI, the Epigenomics “Upload” page (Figure 1B) contains fields for entering important metadata information as well as the dataset itself into the system.
Figure 1. A) The Epigenomics homepage has links for lots of helpful information and tools including the “Upload Tracks” feature. B) The “Upload” page contains a form for the input of relevant information about the dataset. Required information (a) includes Track name, File type, Dataset from either in an uploadable file or a public URL, Species & Genome assembly to serve as the framework for the alignment, and Feature type – specific histone modifications (e.g. H3K4me3, H3K27me3), DNA methylation, chromatin accessibility and more. Additional optional metadata fields (b) are also available for the user to store information which can be used for quick comparisons with other samples in the system.
Each user-uploaded dataset is listed in the “My Uploads” collection as an experiment (Figure 2A). This allows for uploaded data tracks to be selected for operations such as adding to user-created collections or viewing in concert with other database tracks in the customizable genome viewer interface (Figure 2B).
Figure 2. A) User-uploaded datasets are listed in the “My Uploads” collection and shown as independent experiments with supplied metadata, such as cell type, tissue type, differentiation state, etc. These are displayed in the filterable and sortable “Experiments” table. Using the check boxes, at left, to select tracks of interest and clicking “View on Genome” will open a window with the tracks in a customizable genome viewer. B) The uploaded data are shown at the top with user-provided Track names and directly comparable to selected Epigenomics experiment tracks, as well as other NCBI tracks containing Gene annotation, Genome-wide association study, Cited variant, and CpG island information.
FOR MORE INFORMATION:
- Uploading Epigenomics DataSets – YouTube Video | HelpDoc
- Using the Epigenomics Genome Viewer – YouTube Video | HelpDoc
Understanding nature’s mute but elegant language of living cells is the quest of modern molecular biology. From an alphabet of only four letters representing the chemical subunits of DNA emerges a syntax of life processes whose most complex expression is man. The unraveling and use of this “alphabet” to form new “words and phrases” is a central focus of the field of molecular biology. The staggering volume of molecular data and its cryptic and subtle patterns have led to an absolute requirement for computerized databases and analysis tools. The challenge is in finding new approaches to deal with the volume and complexity of data and in providing researchers with better access to analysis and computing tools to advance understanding of our genetic legacy and its role in health and disease.
NOW if our government could synchronize along with the commoners and foreigners to realize and raise awareness that living cells do not stop living outside of the lap or microscope.