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

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 accepts genetic data and the associated quality scores produced by all next generation sequencing technologies including LS454, IonTorrent, Illumina, SOLiD, and Helicos.
Data submission process in NODE consists of four steps, including "submit raw data", "archiving", "submit metadata", and "complete". The arrow bar shown in the following page indicates each step of the submission process by highlighting the specific step.

NODE provides four different ways of data upload, including "Sequence entry", "Http upload", "Ftp upload" and "Express hard drive".
  • 1. Sequence entry
          Input sequences into the blank area directly and then upload them to NODE. Submission of sequences less than or equal to 2MB. This method of uploading data is very convenient if the user has very little data to transfer to NODE.

  • 2. Http upload
          Upload data via website. Submission of sequence files less than or equal to 100MB. This method of uploading data is very suitable for someone who has a small amount data to transfer to NODE.

  • 3. Ftp upload
          If data is too large to upload to NODE by the above two ways, user can apply for the Ftp upload. After the Ftp upload is authorized by NODE, user can upload data to specific Ftp site provided by NODE.
          1) Enter the FTP address

          2) Input the username and password to upload data in your FTP connection tool.
          3) Once the data is uploaded, you can click the "Transfer to Unarchived data" button to move the data to your account. Then you can find the data in the unarchived data.

  • 4. Express hard drive
          Due to network condition, massive scale of data may not be safely uploaded. User could post data to NODE by using hard drive. Before post, please inform us in advance and fill the data collection table which can be download from the following page. After post, please provide us 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

My Project section shows the basic information of user's uploaded project. After clicking "My Project", 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 project. Also, user can use "Create New Project" function to fill the metadata of new project that he/she wants to submit to NODE.
The following image is the metadata information of one project. Through the interface, the user could edit all metadata of the current project. The user could also delete, share, review, download and changing the security status of the project. All the function described as above can be functional by using the buttons in the red rectangle in the following image.
In the project information section, user could skim the brief metadata of the experiments, samples and runs associated with the current project. User could view the detail metadata of experiments, samples and runs related to this project by clicking each ID number. The metadata information of experiments, samples and runs could be edited as well. User could further delete, share, review, download or change the security status of the experiments, samples and runs by using the buttons in detail page of them. If user needs the explanation of detail information of project, experiment, sample and run section, please refer to the document named "Archives (Submit Metadata)".

Data/Metadata Security

NODE provides three levels of data security, including public data, restricted data, and private data. Public data can be searched, visited and downloaded by everyone using NODE. Restricted data can only be searched using the search function in NODE. If you want to visit or download this part of data, you have to ask for the data owner’s permission. Private data can only be seen by data owner.
Once you have uploaded your data, it is automatically considered as private data unless you change its security level. Please be aware that NODE only allows the transformation of data from high security level to low security level. For example, you can only change private data to restricted data or public data, otherwise is not allowed. Also, you can transfer restricted data to public data, but not transfer public data to restricted data.

Change of data security in NODE (Only data owner can do the following changes)

  • 1. Private->Restricted
    The data owner has two ways to change the security of data from private to restricted. He/she can use "security" function beneath each project in the project list to change the security level of data.

    Or he/she can enter the detail page of project, experiment, sample, run or data to use the "security" function to change the security level of data. The same with experiment, sample, run and data.

    Once the data owner changes the security level of data from private to restricted, he/she has stepped to share data. Data will be available in NODE to be searched. However, other users still cannot visit or download the data. On one hand, by using the "until" function, the data owner can select how long that he/she wants to keep data restricted. Data will be automatically public when it has reached the limitation of protection time. On the other hand, if data owner activates "require request" function, other users have to apply for authorization to ask for the access of the data. The data owner can still decide to decline or permit their request.

    After you decide how you want to keep your data, you can click the "confirm", and NODE will show up the further confirmation of the change of your data status which is shown as below:

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

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

    We encourage you to share your data so that you can make your research known by other scientists as well as help other scientists with their research.
  • 2. Private->Public
    Once you change the security level of your data from restricted to public, which means anyone login 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
    The way changing the security status from restricted to public is the same as change the security status from private to public.

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 be shared
    Sharing your data with other researchers is crucial to make your research known by other scientists as well as help other scientists with their research. In the detail page of project, the user can use share button circled by red ellipse shown in the following picture. The similar share button can be found in the detail pages of sample, experiment and run as well.

    After clicking the share button, the user can select which part of the data he/she wants to share by clicking the corresponding box in front of project, experiment, run or data, and enter the email addresses of the person that he/she wants to share this part of data. Once the user confirms the data he/she wants to share, the "My Share" page will show up. The user can see all the shared data. All input email addresses should be registered in NODE.

    In my share page, the user can see all the share data. The sharing 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.

    Then they can check the shared data in "Share From Others" and download data they are interested in by clicking the download button in blue.

  • 2. Review the data
    When data owner wants to publicize data, this function is very useful to make data visible to reviewers. In detail page of project, user can use review button circled by red ellipse shown in the following picture. The similar review button can be found in detail pages of sample, experiment and run as well.

    User can use this function to select the particular person that he/she wants to show the data by inputting the name of the person, the email address and the period that he/she wants the data be reviewed. Also, the user can select which part of the data he/she wants to be reviewed via clicking the corresponding box in front of project, experiment, run or data.

    Once the user confirms the data he/she wants to be reviewed, the "My review" page will show up. He/She can see all the reviewed data.

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 NODEP00278991, shown as below:

User B can search this restricted data called NODEP00278991, but cannot visit or download it:

If user B want to visit this data, user B has to apply for owner’s authorization by sending a request. User B can select which part of this 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 three months. User B just has to simply input the verification code to access to the data authorized by user A.

No matter this request is declined or authorized, user B will receive an email from NODE to know the condition of the application.
1) Request is declined

2) Request is authorized

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 102227 results. On the right panel of the result page, user can find the calculation of results number according to NODE TYPE, TAXONOMY, FLATFORM, STRATEGY and SOURCE for further filter of search results.

If you are interested all projects related to DNA, you just have to simply click project and all 1821 projects will be displayed.

Some tips:

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.

Data Download

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

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

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

    Here is the example of the link for the specific data "pCDNA-ctl_S1-R1.fastq.bz2".

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.

FAQ

Coming soon