Sign up for NODE and Login

Sign up for NODE

  • 1.Register for NODE
    Enter your email address, password and confirm password to register to NODE.

  • 2. User information
    In this section, the user information including first name, last name, organization and country/region are required. while the other information only has to be provided according to user’s interests. Finish the detail information of your account and click “Save”. Your registration is done perfectly in NODE.

  • 3. Registration is done
    Your registration is done in NODE.

  • 4. Acitive your account
    Then you will receive a registration activation link in your registed email box from NODE. Click the link within 48 hours to acitive your account

  • 5. Activation is done
    After the activation, you will be reminded that you have done all steps of your registration. You can start to login NODE.

Some tips:

  • 1. Please use a new and valid email address and enter email address properly for registration. Or you will get the following reminders:
          1) Email registered

  •       2) Not a valid email

Login to NODE account

After the registration, user can login to NODE by inputting proper email address and password in the login page. NODE provides “Remember Password” function so that user doesn’t have to input email address and password every time using NODE. We suggest that you ONLY activate this function in your personal computer.

Some tips:

If you forget your password, you can simply click “Forget Password” and input your email address in the following page and click send to send password reset to your email.

Here is the email example received from NODE for the reset of the password.

Click “Password Reset”, user can reach the password reset page in NODE. To keep your account safe, we strongly encourage you NOT to share your password.

Data Upload/Transfer

NODE (The National Omics Data Encyclopedia) provides an integrated, compatible, comparable, and scalable multi-omics resource platform that supports flexible data management and effective data release. NODE uses a hierarchical data architecture to support storage of muti-omics data including sequencing data, MS based proteomics data, MS or NMR based metabolomics data, and fluorescence imaging data.
The data submission process in NODE consists of three steps, including "Submit raw data", "Submit metadata" and "Archiving". The arrow bar on the following page indicates each step of the submission process by highlighting the specific step.

NODE provides three different ways for data uploading, including, "Http upload", "FTP upload" and "Express hard drive".
  • 1. Http upload
         Uploading data via website for files less than 100MB. This method of uploading data is very suitable for someone who has a small amount of data to transfer to NODE.

  • 2. Sftp upload
         If data is too large to upload to NODE using http, users can apply for the Sftp upload. The Sftp account and password is the user's email and password for logging into NODE.

          1) FTP tools:
          We recommend using FTP client software to upload files, e.g., FileZilla
    •       • Host: fms.biosino.org
    •       • Username: NODE username (email)
    •       • Password: NODE password
    •       • Port: 44398

          2) Command line:
          SFTP
    sftp   -oPort=44397   your-node-register-email@fms.biosino.org
          Password: your-node-password
          Navigate to the target folder you need
    #Navigate to the target folder
    put  example.fastq.gz
          LFTP
    lftp
    lftp  :~>  connect  sftp://fms.biosino.org:44397
    lftp  fms.biosino.org:~>  your-node-register-email
          Password: your-node-password
          You can use mput to upload data
    mput  *.gz
          Once the data is uploaded, you can click the "Preload datalist" button to find the data in your account.

  • 3. Express hard drive
          Due to network condition, massive scale of data may not be safely uploaded. Users can post data to NODE by using hard drive. Before posting, please inform us in advance (+86 021-54920550). After posting, please provide us with the details of your post. Our contact information is as below:
          Email address: node-support@picb.ac.cn
          Address: Bio-Med Big Data Center, 320 Yue Yang Road, Shanghai, 200031 P.R.China

Archives (Submit Metadata)

After successfully uploaded, data would be in unarchived status. We STRONGLY encourage users to fill metadata as completed as possible after unloading data. This information is crucial if you want your data to be searched and visited, and share your data with other researchers. In NODE, user could use the “One Step Archiving” function to arrange the metadata information, including Project,Experiment,Sample,Run,Submitter.

There are two types of data archiving forms: raw data and analysis data archiving. Raw data archiving are mainly used to archive metadata, and analysis data archiving are applied to archive data analyzed by different kinds of software or tools.
When clicking the Raw Data button, the user will enter the metadata archiving interface.

Here is some guidance for filling detail metadata information of each part.

Project:

Project name: NODE allows users to add data to existed project or create new project name.
Project security status: NODE provides six levels of security options for your project, including private, restrict for one month, restrict for three months, restrict for six months, require request and public. Please choose the right security status of your project based on your request.
Description: the description of the project
Related links: links to resources related to this project (publication, datasets, online databases). User could use the plus button to add more links based on the project.

Experiment:

Experiment name: NODE allows users to add the data to existed experiment or create new experiment name.
Experiment security status: NODE provides six levels of security options for your experiment, including private, restrict for one month, restrict for three months, restrict for six months, require request and public. Please choose the right security status of your project based on your request.
Experiment description: the description of the experiment.
Experiment design: the information of the strategy of the experiment.
Platform: the platform that the user used to do the experiment, NODE provides six different options, including Illumina Hiseq 2000, Illumina Hiseq 2500, Illumina Hiseq 3000, ABI SOLiD 3, ABI SOLiD 4 and Illumina Miseq. Please select the correct platform according to your experimental design.
Planned read length: the user could input the planned read length according to his/her experiment
Mate pair: the user could choose Y/N base on his/her data.
Library name: the user can define a name for his/her library
Library_strategy: sequencing technique intended for this library. NODE provides five options, including WGS, EST, RNA-Seq, FINISHING, Chip-Seq. Please select the correct library strategy according to your experimental design.
Library_source: specifies the type of source material that is being sequenced. NODE provides three options for selection, including genomic, transcriptomic, metagenomic. Please select the correct library source according to your experimental design.
Library_selection: method used to enrich the target in the sequence library preparation. NOED provides three options including PCR, RT-PCR and RANDOM. Please select the correct library source according to your experimental design.
Library_layout: the way how the sequence is amplified. NODE provides three options including single, paired, targeted_loci. Please select the correct library source according to your experimental design.
Library_construction: briefly describe the way how the user constructed the library.
Related_links: related links for your experiment, user could use the plus button to add more links based on your experiment.

Sample:

Sample_name: NODE allows users to add the data to existed sample or create new sample name.
Sample taxonomy: the user could fill tax_id or taxonomy of the sample he/she used.
Sample Organism: the organism the user used to prepare the sample, eg : liver, means this sample is get from liver. or in general from human.
Sample description: the description of the sample
Sample attributes: if there is any other information related to the sample that the user can not fill in any part of the sample table, please put in the sample attributes part. The user could user plus or minus button to add or delete attributes, respectively.
Sample provider: the information of the people who provided the sample for the experimental analysis.
Related links: links to resources related to this sample or sample set (publication, datasets, online databases). User could use the plus button to add more links based on your sample.

Run:

Run name: NODE allows users to add the data to existed run or create new run name.
Run security status: NODE provides six levels of security options for your run, including private, restrict for one month, restrict for three months, restrict for six months, require request and public. Please choose the right security status of your run based on your request.
Description: the description of the run.
Related links: Links to resources related to this RUN or RUN set (publication, datasets, online databases). User could use the plus button to add more links based on the run.
When clicking the Analysis Data button, the user will enter the analysis data archiving interface.

Here is some guidance for filling analysis data information.

Analysis name: NODE allows users to add the data to existed analysis or create new analysis name.
Analysis security status: NODE provides six levels of security options for your analysis, including private, restrict for one month, restrict for three months, restrict for six months, require request and public. Please choose the right security status of your run based on your request.
Analysis description: the description of the analysis.
Program: the name of software or tools to analyze the data.
Link: links to resources related to the analysis step.
Version: the version of the program.
Nodes: notes for the analysis step.
Output: select the corresponding data ID of the analysis data
Target: associate data with projects, experiments, samples, runs, data and analysis by clicking each ID number

Submitter:

First name: the given name of the submitter
Last name: the submitter’s family name
Organization: the name of the organization where the submitter worked, eg SCBIT
Email: the valid email address of the submitter
Country/Region: the country or the region where the submitter from.
After user finishes filling all parts as described above, he/she can preview the detail on the right panel and click save if all information is correct. However, if user doesn’t fill any information, NODE will automatically distribute project name, experiment name, sample name and run name. Data is private after being archived if user doesn’t choose any security status while doing the “One Step Archiving”. User can finish all the information later. Here, we show examples as below that user successfully archived his/her using “One Step Archiving” function in NODE.

Some tips:

  • 1. Data is immediately available in our website if user archives data as public or restricted. However, data can ONLY be searched in the second day if user archives data as public or restricted before 15:00 (local time in Beijing) due to NODE system update. If user archives data later than 15:00 (local time in Beijing), data can only be searched the third day after archiving.
  • 2. User can also fill the metadata for his/her project, experiment, sample, run by using “Creat New Project”, “Creat New Experiment”, “Creat New Sample” and “Creat New Run” in the pages of “My Project”, “My Experiment”, “My Sample” and “My Run”, respectively.

NODE Architecture

NODE is a biological big data collection platform, including the experimental sample information collection, the file upload of the sequences, and the analysis, share and download of the results. NODE platform consists of six main modules: project, sample, experiment, run, data, and analysis. Project and Sample are independent of each other, but can be linked through Run. In this way, the metadata and sequence information can be integrated.

Data/Metadata Management

The My Project section displays the basic information of the user's uploaded project. After clicking "My Project", the user can view all the uploaded project list pages. In the Project List page, user can click each project and view the details of metadata information of different projects. Also, the user can use the "Create New Project" function to fill in the metadata of a new project that he/she wants to submit to the NODE.
The following picture shows the metadata information of a project. Through the interface, the user could edit all the metadata of the current project. The user could also delete, share, review, download and change the security status of the data. All the functions described above could be performed by using the buttons in the red rectangle in the following figure.
In the project information section, the user could browse the short metadata of the experiments, samples and runs associated with the current project. The user could view the detailed metadata of the experiments, samples and runs associated with this project by clicking on each ID number. The metadata information of experiments, samples and runs could also be edited. The user could also delete, share, review, download or change the security status of the experiments, samples and runs by using the buttons on the detail page of them. If the user needs the explanation of the detailed information of the project, experiment, sample and run section, please refer to the document named "Archives (Submit Metadata)".

Data/Metadata Security

NODE offers three levels of data security, including public data, restricted data and private data. Public data can be searched, viewed and downloaded by anyone using NODE. Restricted data can only be searched using the search function in NODE. If you want to visit or download this part of the data, you need to get permission from the data owner. Private data can only be viewed by the data owner.
Once you have uploaded your data, it is automatically considered private unless you change its security level. Please note that the NODE only allows data to be converted from a high security level to a low security level. For example, you can only change private data to restricted data or public data, otherwise it is not allowed. You can also convert restricted data to public data, but not public data to restricted data.

Change of data security in NODE

NODE encourages users to share your data so that other scientists can find out about your research and help other scientists with their research.
Note: Only the data owner can make the following changes
  • 1. Private->Restricted
    As the owner of the data, there are two ways to change the security of the data from private to restricted. You can use the "Security" function under each project in the project list to change the security level of the data.

    Or you can go to the Project, Experiment, Sample, Run or Data detail page and use the Security function to change the security level of the data. The same applies to Experiment, Sample, Run and Data.

    Once you change the security level of the data from Private to Restricted, you have taken the step of sharing the data. The data will be available for browsing on the NODE. However, other users will still not be able to view or download the data. On the other hand, you can use the "until" function to choose how long you want to keep the data restricted, one year or two years. At the end of this period, the data will automatically be released. On the other hand, if you activate the "require request" function, other users will have to apply for authorisation to request access to the data.

    Once you have decided how you want to keep your data, you can click "Confirm" and the NODE will display another confirmation of your data status change, as shown below:

    If the security status is successfully changed, the security of the data is restricted.

    Other users can send a request to ask the owner for permission to use restricted data.

  • 2. Private->Public
    Once you change the security level of your data from restricted to public, which means anyone logging to NODE can search, visit and download your data. Also, NODE will show up a confirmation for you to reconfirm the security status of your data.

    If the security status is successfully changed, the security of the data will become public.

  • 3. Restricted->Public
    Changing the security status from restricted to public is the same as changing the security status from private to public.
    If the security level of the data is changed from Private to Restricted or Public, the visibility of Projects, Experiments, Samples and Runs will change from Inaccessible to Accessible, i.e. other NODE users will be able to view the relevant information.
    Tips: You can cascade at any level of Projects, Experiments, Samples and Runs to change the security level of all data below that level.
    Project level

    Experiment level

    Sample level

    Run level

Some tips:

The following three ways of changing the security status of data are NOT allowed by NODE. If you have to do the following changes, please contact NODE_support@picb.ac.cn
  • 1. Public-------->Private
  • 2. Public-------->Restricted
  • 3. Restricted -------->Private

The “Domino effect” of the security change

NODE platform consists of six main modules: project, sample, experiment, run, data, and analysis. Project and Sample are independent of each other, but can be linked through Run. In this way, the metadata and sequence information can be integrated. The change of security levels obeys the flow of NODE architecture and the security change of the upstream of this flow will bring up the security change of downstream of this flow. The following four examples can help users to understand this rule in details.

Example 1:
When the security level of project is changed, the experiment, sample, run and data related to this project will all show up for the change of security. You can still decide what kind of information of this project you want to keep by yourself, and you just simply bin it from the “security status change confirmation”. The function of bin is marked with red square in the following picture.

Example 2:
The change of the security level of experiment will bring up the corresponding sample, run and data for the security change. You can decide the security status the same way as example 1.

Example 3:
The change of the security level of sample will bring up the corresponding run and data. You can decide the security status the same way as example 1.

Example 4:
The change of the security level of run will only bring up the corresponding data. You can decide the security status the same way as example 1.

Share and Review

  • 1. Sharing the data and being shared
    Sharing your data with other researchers is crucial to make your research known to other scientists and to help other scientists with their research. On the Project Details page, you can use the Share button, which is surrounded by a red ellipse, as shown in the image below. A similar Share button can also be found on the Sample, Experiment and Run detail pages.

    After clicking on the Share button, you can select which part of the data to share by clicking on the corresponding box in front of Project, Experiment, Run or Data and enter the email addresses of the person(s) with whom you wish to share this part of the data. The user can see all the data that has been shared on the following "My Share" page. Persons being shared needs to be a registered NODE user.

    On the My Shares page you can see all your shared data. The share button in green can be used to unshare the data.

    Users that are shared of data will receive an email from NODE to inform the successful share of data.

    They can then review the shared data under "Share From Others" and download the data they are interested in by clicking the download button in blue.

  • 2. Review the data
    If data owner wants to publish data, this feature is very useful to make data visible to reviewers. On the detail page of the project, the user can use the review button surrounded by a red ellipse as shown in the following picture. The similar review button can also be found in the sample, experiment and run detail pages.

    The user can use this feature to select the specific person to view the data by entering the person's name, email address and the period of time they wish to view the data. The user can also select which part of the data he/she wishes to review by clicking on the appropriate box in front of Project, Experiment, Run or Data.

    Once you have confirmed the data to be reviewed, the "My Review" page is displayed. You can see all the data that has been checked.

Request for Restricted Data

You have to apply for the authorization from author to use restricted data.
For example:
User A has restricted data in NODE called OEP000773, shown as below:

User B can search this restricted data called OEP000773, and visit it, but cannot download it:

If user B want to download the data, user B has to apply for owner’s authorization by sending a request. User B can select which part of the data is required and wait for user A’s permission.

User B can check my requests in user center.

Then user A will receive an email from NODE shown as below:

User A can check the requests from others in user center.

User A can login to NODE and find the data request in user center to permit or decline this request.

If user A authorize this request, user B will receive a verification code which lasts for one month. User B just simply clicks ID to jump to the download page, and clicks Export Data Links to get the download address.

NODE Search

NODE provides full text search. Although results searched by NODE will not be very precise, user can get all information related to the keyword inputted for search. User can use the information in right panel to further reach the detail information which he/she is interested in. For example, if the user searches "DNA" in NODE, he/she can get totally 677 results. On the right panel of the result page, user can find the calculation of results number according to NODE TYPE, and ORGANISM for further filter of search results.

If you are interested all experiments related to DNA, you just have to simply click experiment and all 28 experiments will be displayed.

1. View and management of data

User can check the data list by licking "My Data" in the drop-down box at the top right corner, and then some examples of uploaded data and the information related to data, such as file name, file size, security status and the date the file uploaded are displayed. Here is the list of archived files.

2. View and management of the project

User can check the project list by clicking "My Project" in the drop-down box at the top right corner, and then some examples of uploaded projects and the information related to these projects, such as project name, data security status and the date the project uploaded are displayed. Here is the list of uploaded projects.

3. View and management of the experiment

User can check the experiment list by clicking "My Experiment" in the drop-down box at the top right corner, and then some examples of uploaded experiments and the information related to these experiments, such as experiment name, data security status and the date the experiment uploaded are displayed. Here is the list of uploaded experiments.

4. View and management of the sample

User can check the sample list by clicking "My Sample" in the drop-down box at the top right corner, and then some examples of uploaded samples and the information related to these samples, such as sample name, data security status and the date the sample uploaded are displayed. Here is the list of uploaded samples.

5. View and management of the run

User can check the run list by clicking the "My Run" in the drop-down box at the top right corner, and then some examples of uploaded runs and the information related to these runs, such as run name, data security status, the experiment related to each run and the date the run uploaded are displayed. Here is the list of uploaded runs.

Data Download

1. HTTP download

  • 1) Bulk Download
    Download all links related to one project by using the "Download" function in NODE. This function is highly recommended for the download of large amounts of data.

    Here is the example of all links for data related to the project "OEP000035".

  • 2) Download specific data
    Download files one by one by clicking the download button. This function is more likely to be used to download the specific data which is interested by the researcher.

2. FTP download

Tips:
The data download directory is arranged according to the Run id, in the form of /Public/byrun/OER/OER/OER.
“byRun” is for rawdata download
“byAnalysis” is for analysis data download
Where can I get the run list?
Using “Export data links” in project detail page.

  • 1) Windows
    We recommend using FTP client software to upload files, e.g., FileZilla
    • • Host: fms.biosino.org
    • • Username: NODE username (email)
    • • Password: NODE password
    • • Port: 44398
    Click on the “Quickconnect” for data download.

  • 2) Linux
    SFTP
    sftp   -oPort=44398   your-node-register-email@fms.biosino.org
    Password: your-node-password
    Navigate to the target folder you need
    cd  /Public/byrun/OER**/OER****/OER****** get  example.fastq.gz
    LFTP
    lftp
    lftp  :~>  connect  sftp://fms.biosino.org:44398
    lftp  fms.biosino.org:~>  your-node-register-email
    Password: your-node-password
    You can use glob pget or mget to download data
    glob  pget  /Public/byrun/OER**/OER****/OER******/*.gz
    mget  /Public/byrun/OER**/OER****/OER******/*.gz

User Center

User center is a convenient tool for user to have an overview of his/her own NODE data as well as management of data request.

In the following part of user center, user can have an overview of NODE data, the detail information of the user and highly accessed publications related to the research with high access rate in NODE, as well as other convenient function for the share and use of the data, such as ”My shares”, ”Share From Others” , “My Requests”, ”Requests From Others”, ”My Reviews” and ”Analyze”.
”Amount of Data” present the numbers of projects, experiments, samples, runs, analysis and data of the user according to three security status respectively. ”Views of Data” display the numbers of user's data with graphs in different months and as well as nearly one week, nearly one month, nearly three months. In the map on the right, you could see which country the data are from in the world. ”Download of Data” display the download times of user's data with graphs in different months and as well as nearly one week, nearly one month, nearly three months.

” My data list” show all the data of the user, including projects, experiments, samples, runs, analysis and data. Besides, some examples of uploaded data and the information related to these data, such as data name, security status and the uploaded date are displayed. And relevant classified statistics including data category, security, platform, taxonomy of the data are shown in the red box on the right.

Furthermore, you can input the filter words and period time to search your data, and then the filtered data list are shown in the red box on the left.

Here, we show some examples of the NODE data.

1. View and management of data
User can check the data list by licking “My Data” in the drop-down box at the top right corner, and then some examples of uploaded data and the information related to data, such as file name, file size, security status and the date the file uploaded are displayed. Here is the list of archived files.

2. View and management of the project
User can check the project list by clicking “My Project” in the drop-down box at the top right corner, and then some examples of uploaded projects and the information related to these projects, such as project name, security status and the date the project uploaded are displayed. Here is the list of uploaded projects.

3. View and management of the experiment
User can check the experiment list by clicking “My Experiment” in the drop-down box at the top right corner, and then some examples of uploaded experiments and the information related to these experiments, such as experiment name, security status and the date the experiment uploaded are displayed. Here is the list of uploaded experiments.

4. View and management of the sample
User can check the sample list by clicking “My Sample” in the drop-down box at the top right corner, and then some examples of uploaded samples and the information related to these samples, such as sample name, security status and the date the sample uploaded are displayed. Here is the list of uploaded samples.

5. View and management of the run
User can check the run list by clicking the “My Run” in the drop-down box at the top right corner, and then some examples of uploaded runs and the information related to these runs, such as run name, security status, the experiment related to each run and the date the run uploaded are displayed. Here is the list of uploaded runs.

Release of human genetic resources

We expect you to comply with applicable laws or regulations if you plan to submit the data that contains human genetic information to us. Please also make sure your submitted data is set to RESTRICTED status by using our data submission tool. In addition, your submission should not breach participating individuals’ rights and comprise their original signed consents. http://www.gov.cn/zhengce/content/2019-06/10/content_5398829.htm

FAQ

Coming soon