Category: DocumentationThe news items published under this category are as follows.
Posted by: admin on Wednesday, March 02, 2005 - 08:26 PM
OPMD_DOC
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Posted by: admin on Tuesday, March 01, 2005 - 10:21 PM
BROP_DOC
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The high-frequency automatic genome annotation pipeline:
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Posted by: admin on Tuesday, March 01, 2005 - 06:03 PM
BROP_DOC
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Site Statistics of BROP
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Posted by: admin on Tuesday, March 01, 2005 - 06:02 PM
BROP_DOC
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The Discussion Forum of BROP
User's feedback is very important in the software design. We believe in designing the bioinformatics software that make sense to biologists and the most useful approach in doing this is through communication with the end users - the biologists. A piece of software, no matter how useful and how many functionalities it has, is deemed useless unless two criteria are matched:
1. The design and use of the software is intuitive to biologists (not compuer scientists)
2. The software is well-documented and help or user's guide can be conveniently found where it is supposed to.
Many of the BROP software were developed in response to users' feedback. In fact the reason that BROP exists is because of the need of tools by some biologists, in particular researchers at The Forsyth Institute in the begging stage. Thus we welcome your input/feedback/comment/suggestion. Whatever idea you have, let us know and we'll try to improve or accomodate the options in the BROP tools.
User's feedback is welcome through email, however we strongly encourage feedback through the discussion forum system so that the ideas can be shared among users and similar ideas or questions won't need to be addressed repeadedly.
In time if the forum is frequently used, it will become a good information source itself. The discussion has a search function so whenever a user has a question, the discussion forum can be the first place to look for answers - someone may already asked a similar question or post a similar idea.
To prevend from spam message posting, you have to be a registered user to post message.
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Posted by: admin on Tuesday, March 01, 2005 - 06:01 PM
BROP_DOC
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Microbial Genome Codon Usage Database
The MGCUD is a project that focuses on analyzing the global codon usage patterns of all NCBI microbial genomes.
It is temporarily resided in the BROP site although it has its own web address at http://codonusage.forsyth.org. A manuscript is under preparation. More detail user's guide will be available here as well as the above web site.
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Posted by: admin on Tuesday, March 01, 2005 - 06:01 PM
BROP_DOC
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Oral Pathogen Entrez Counter (OPEC)
OPEC is a simple tool that monitors the number of database records (publications, sequences, data, etc) in NCBI Entrez database. Every morning 4 a.m. (Eastern Standard Time) this program automatically updates the total number of the Entrez database record for each oral pathogen genomes.
Note that in OPEC, in order to cover most records, the species name of the genome (e.g., Porphyromonas gingivalis) is used as the keyword in the "term" field. That is, any record that has the keyword (e.g., Porphyromonas gingivalis) in all fields will be counted. The search could have been done specifically in the field "Organism" but some data records do not have this field. In the future if we see that specific search in the "Organism" field is more useful, we will modify the script to do so.
When you click the OPEC link, a summary table will be shown which give a total number of all kinds of data records found in NCBI Entrez. Clicking the number will lead to a detail list that shows how many records are found in which dataset in a time-incremental way (if that particular database allows to search based on the date, i.e., all, past 6 months, 3 months, 1 month, 1 week, day etc). These numbers are linked to NCBI Entrez for detail records.
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Posted by: admin on Tuesday, March 01, 2005 - 06:00 PM
BROP_DOC
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The Oral Pathogen Microarray Database (OPMD) serves as a public data repository center for the microarray data that were used to study oral pathogens.
Below is a list of user's guides in OPMD:
- The databases of OPMD
- Downloadable raw microarray data submitted by authors for publication.
- Searchable microarray database
- The analysis tools of OPMD:
- Links, links, links.
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Posted by: admin on Tuesday, March 01, 2005 - 05:59 PM
BROP_DOC
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There are as many starting/entry points as the number of tools available at BROP. This is particularly true for Genomics Tools. Here is a list of different web pages or links that you can get to the genomics tools:
- The BROP home page (http://www.brop.org) - click the"Genomics Tools for Oral Pathogens" menu item on the left panel.
- Direct web address to the top page of the genomics tools - http://genome.brop.org
- Start from a special navigation interface called "Genome Explorer" (GenomeExp) - starting from selecting either "Oral Pathogens" or "NCBI microbial genomes", then select an organism. A list of all the tools (shown as icons) will be shown that are available for the selected genomes.
The top page of the genomics tools - genome.brop.org shows a list of all the major tools available for the oral pathogens. Afte rall the focus of BROP is on genomics of oral pathogens, this table is provided for the convenience of the researchers who study oral pathogens. However BROP also includes useful tools for analyzing all NCBI microbial genomes and they can be selected using the Genome Explorer interface.
Below is a list of user's guide to all the Genomics Tools and imporant information available at BROP:
- Text-searching the annotation databases at BROP
- Genome Viewer (GenomeView)
- Automatic KEGG metabolic pathway mapping
- Automatic Gene Ontology mapping
- GOAL - Genomewide ORF Alignment
- Sequency homology search using BLAST
- Domain homology search
- The high-frequency automatic genome annotation pipeline
- Links, links, links
- When is the data last updated? Checking the dates and status of the annotation servers
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Posted by: admin on Tuesday, March 01, 2005 - 05:59 PM
BROP_DOC
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This section describes the feature of the BROP home page - how the page items are arranged and useful links that you may not notice.
The following figure depicts all the useful features:
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