BioCode (https://ngdc.cncb.ac.cn/biocode) serves as a centralized repository dedicated to archiving bioinformatics tool codes for open-source projects.
This platform hosts an extensive collection of bioinformatics tools developed for diverse data analysis purposes, accompanied by detailed metadata for each tool.
The metadata includes the tool's name, description, category, associated grants, publications, citation counts, contact information for the tool owner,
and organizational affiliations. As of August 2024, BioCode has archived a total of 7,310 bioinformatics tools, sourced through user submissions and
automated literature curation from leading journals in the bioinformatics field, such as Bioinformatics, BMC Bioinformatics, Genome Biology,
and Nucleic Acids Research.
BioCode enables any user to submit their tools, positioning itself as a vital archival hub where bioinformatics tool developers can host their code,
software packages, documentation, and related metadata. This centralized archiving approach significantly enhances the accessibility and
discoverability of bioinformatics tools, making them publicly available and searchable. Consequently, BioCode functions as an open content platform,
facilitating both tool developers in the dissemination and preservation of their tools, and tool users in the efficient browsing, searching,
and downloading of tools relevant to their research interests.
1. How to submit the bioinformatics tools?
1.1 Access the tool submission page
Only registered users are allowed to submit new tool in BioCode.
Click the 'Sign Up / Sign in' button on the right side of the top navigation bar to register and log in,
and click the 'Submit Tool' button on the navigation bar to enter the tool submission page.
1.2 Fill in the general information of tool
Fill in the general information about the tool and click the 'Save and Next' button to proceed the next step.
1.3 Fill in grants information
Click on 'Agency' to select an organisation. Click 'Program' to select a program. Fill in the grant id and title.
If there is no corresponding 'Agency' and 'Program' in the list, you can select 'Other' and fill them manually.
If the tool has no funding support, you can select 'No funding support', examples include:
If you have multiple grants, you can click the 'Add Grant' button to add a new grant form.
Note that all grant forms must be saved by clicking the 'Save' button. Finally, click 'Next Step' to proceed the next step.
1.4 Fill in credits and publications information
If the tool has more than one contributor, you can click the 'Add' button in the upper left corner to fill in and save the credits.
If there are related publications, you can search for them by PMID in the search box on the right and click 'Add' button to add.
1.5 Fill in manual
Fill in the manual of tool. Click the 'Save and Next' button to save and proceed the next step.
1.6 Fill in release and submit tool
Fill in the release information and notes, upload the corresponding code and files of the tool, and then click the 'save' button to save.
If you need to submit a new version, you can click 'add release' in the upper left corner to add a new release.
Finally, click 'Submit Tool' in the bottom left corner to submit the tool.
2. How to search the bioinformatics tools?
Users can use 'Keyword Search' or 'Feature Search' methods to search tools.
Keywords Search
- Method one: you can search tools through keywords in the search module of the index page.
- Method two: click the navigation bar 'Search' to access the tool search page, through the left side of the 'Search' module for the keyword search.
Feature Search
- Click the navigation bar 'Search' to access the tool search page, set search conditions using the 'Advanced Search' module and search through the tool feature conditions.
3. How to browse and download the bioinformatics tools?
3.1 Tool Browse
On the search page, click the name of the tool in the search list to go to the tool details page. On the details page,
you can click the left navigation to switch and view the tool information, tool manual, tool releases and files, and tool statistics.
3.2 Tool Download
Select the version of the tool you need in the 'Download' module and download the files by clicking on the files in the 'File List'.
4. How to score the bioinformatics tools?
Rating
You can rate the tool in the tool details page after logging in. If you are not a registered user,
you can register for an account by clicking the 'Sign Up' button on the right side of the navigation bar.
Click the 'Sign In' button to log in.
Click on the 'Stars' in the rating module to give a score, and click the 'Submit a review' button to submit your review.
5. How to edit the biological databases?
5.1 Browse Tool List
After logging in, you can click the 'My Account' button to enter your Personal Center.
In the Personal Centre, you can see the list of your tools and the status of tools (including Unfinished, Submitted and Released).
You can edit and delete the tool by the button on the right side.
5.2 Edit Tool
Click the 'edit' button to edit the tool, this interface is the same as the tool submission interface.
You can quickly jump to the corresponding information module for modification through the navigation,
after modification, please click the corresponding 'save' button to save.
5.3 Submit Edit
After finishing the editing, click the 'Tool Submit' button at the bottom right corner of 'Release Information' to submit the modified tool.
BioCode: a worldwide centralized repository for archiving bioinformatics tool codes for open-source projects. (in preparation)
National Genomics Data Center,
Beijing Institute of Genomics,
Chinese Academy of Sciences and China National Center for Bioinformation,
Beijing 100101, China
Email: biocode(AT)big.ac.cn
Tel: +86 (10) 84097845