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Workflows and Services

Content of workflows

Workflows are any documents that guide the analysis of any type of biomedical data, which could be, for example,

  • Formal "workflows" defined in some workflow languages
  • Scripts in any scripting language for the analysis of some data
  • Screenshots for the use of certain software or cloud platform
  • A software package written in any language

Format of workflows

In physical form, workflows sold at bioworkflows.com can consist of

  • Meta data such as title, description, keywords, license, price etc
  • Main page that contains description of the workflows, which could include description of the data, scripts, outputs, figures. The main page could be in Jupiter Notebook or RMarkdown format.
  • Banner images one or more images that illustrate the workflow, which could be automatically extracted from the main page if a Jupiter Notebook is supplied.
  • Arbitrary attachments which can include the main "scripts", datasets.

Copyrighted and public-domain workflows

Sellers of workflows can reserve all the copyrights, or put the workflows in public domain. The main difference Is that you can modify or re-distribute workflows in public domain but cannot do so for copyrighted workflows.

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Free and premium workflows

Sellers can sell both copyrighted or public-domain workflows for a price, or distributed them for free.

External workflows are workflows that reside on other websites. We collect basic information about these workflows so that they can be searched by tags and description. Users will be redirected to these websites when viewing the workflow, but we cannot guarantee the availability of these external web resources.

On-site workflows are workflows that users contribute to bioworkflows.com. An on-site workflow contains a "main document" and arbitrary attachments. On-site workflows can be copyright protected and listed for sale, in which case only paid customer can view and download the entire workflow.

Workflows can be in any scripting language and for any platform, and may not even contain any useful instructions (e.g. from sellers who sells only services, not workflows themselves). The method to apply workflows to your data will therefore vary greatly. For example
  • If the workflows contains scripts, you may need to adapt the scripts to your own data for your own computational environments
  • If the workflows contains more or less "portable workflows", you will need to use the appropriate workflow executors and execute the workflows,
  • If the workflows contains screenshots or video tutorials, you could try to follow the step by step guide to analyze your data manually
  • If the workflows use certain proprietary software or platform, you will need to gain access to the software or platform before you try to use them
  • If the workflows are provided only for the demonstration of the process and lacks any detail, you will need to talk to the seller and set up a service agreement for him or her to develop workflows for your particular needs.
It is therefore imperative for you to read the descriptions of the workflows carefully to check if they can be applied to your data. "Keywords" are useful tools for you to filter workflows to identify those that match the platforms and/or tools used.

There are indeed free and publicly available software tools, tutorials, even workflows for almost all tasks for biomedical data analysis. However, the quality of these resources vary greatly and many, if not most of these resources are outdated due to rapid evolution of biomedical research and applications. Workflows offered by BioWorkflows.com can be better because
  • They are supported by their authors so you know who to ask if you get a question
  • They are rated by peer users so you can learn how others apply the workflows before trying them
  • They are updated by their authors so you are not left in the dark when new tools and reference data become available. Note that you are entitled to all future updates of purchased workflows.

Bounties are great ways to increase visibility of your questions and show appreciations to people who help you. To post a bounty, you can
  • Create or locate a question with the question that you are interested,
  • Click Post a Bounty, enter an amount, and duration of the bounty.
  • Click Submit and you will be prompted to pay for the bounty. If you have enough balance in your account, your account will be charged directly.
Your question will be posted and anyone can answer it. You and others can evaluate the answers and upvote and downvote it. At the end of the bounty period, the bounty will be shared by answers according to the number of upvotes (minus downvotes) they received. The following restrictions apply:
  • A minimal amount of required to post a bounty.
  • The duration of the bounty can be between 1 day and 2 months (60 days)
  • You can withdraw a bounty if there is no upvoted answer after 7 days. The bounty will be returned to your balance as store credit. No refund will be issued.
  • Bounties without upvoted answers at the end of the bounty period will be canceled.
  • To avoid abusive use of bounties, only trusted users can up or down vote posts. In addition, up or downvotes from answerers are ignored.

Buying Workflows and Services

Most sellers offer a standard no-question-asked 30-day return guarantee for their workflows. This means you can return the purchase of workflows within 30 days if you cannot make it work.
Things will become a little bit complicated if you purchased a workflow without such a refund policy and the quality of workflow does not meet your expectation. In this case you will need to email our custom support for a refund.

There are a few ways to get help,
  • If the seller offers support to the workflow (this can be a good indicator that the sellers are behind their workflows), you can contact them through the support section of the workflow that you purchased.
  • You can post a comment under the comment section of the workflow so that other buyers can help you. The comments will be viewable by all visitors.
  • It is generally discouraged to post questions about specific workflows in the discussion forum (), but you could ask for recommendations on the right workflows to use, especially if you offer a bounty for your question.
  • If none of the method works, you can leave a negative feedback for your purchase to warn others against the purchase the workflow.

If you are looking for a particular workflow and cannot find any from our website, you can
  • Post a question in our discussion forum (Workflows -> Discussions). Please be very specific about the data or problems you have and what types of workflows you are looking for.
  • You may also search sellers by their expertises (Services -> Expertise or Services -> Freelancers) and contact them directly through one of their offered workflows and related services.
Note that it is very helpful to add keywords to your posts because this will notify all sellers who have relevant expertises. It can be a good idea to set up a bounty to show your appreciation for the help you can get.

Selling at BioWorkflows.com

Thank you for your interest in becoming a seller on BioWorkflows.com. Generally speaking, to become an seller, you will need to
1. Make sure you are eligible to become a freelancer.
If you will only occasionally answer a few questions (and claim some bounties), or you are only interested in distributing your workflows for free, you generally do not need to worry about eligibility. However, if you become serious and would like to provide a number of high quality workflows and providing services, you should make sure that you are eligible to work as a freelancer. It may surprise you that your employer disallows you to work on a second job, especially if what you sell at bioworkflows.com may contain copyrighted material that you develop at work.
2. Register an account and become an seller
After you register an account at BioWorkflows.com, you can go to settings, then become an seller. You will need to agree on our terms of service and acknowledge a few important notices such as copyright of workflows. In some rare cases, we may contact your for additional verification. You will also need to set up one or more payout methods for you to receive payments, and it is highly recommended that you create "expertises" and make your profile publicly available so that others can locate you from these expertises.
3. Create workflows and advertise your services
There are several method for you to provide services. You can
  • Create workflows and charge a price for the sell of each copy to it.
  • Offer to provide paid services for selected workflows.
  • Answer questions in our discussion forum, and claim bounty either by answering the questions directly or referring to your own workflows

Once you have uploaded a workflow (My Workflows -> Upload), the workflow is in draft mode and can be freely modified.
  • You can edit the workflow by modifying its meta data, main page, and add or remove attachments
  • If you have set up GitHub integration to your workflow, pushing to the GitHub repository will automatically update the workflow on bioworkflows.com.
After you are satisfied with your workflow, you can submit the workflow for review. The reviewer may return the workflows to you for additional revision. If the workflow is approved for publication, it will be available to public shortly.

The simply answer is you cannot. Workflows cannot be altered in anyway (except for certain meta data such as keywords) once they are published. You can however always fork your workflow to create a newer version.
  • After you publish a forked workflow, the newer version will become the default version.
  • The old version are still available from the workflow details page. In this way you can create a variations of the same workflow (e.g. one for mouse and one for human) and you even set the name of the variants to make them easier to remember.
  • You can opt to archive the old version of the workflow. In this case the workflows will not be listed under the details page, but will still be available to buyers of the workflows.
If you have set up GitHub integration to the workflow, pushing to a published workflow will automatically create a new version of the workflow in draft mode.

All sales are final after 30 days so you can only withdraw funds from workflows that you sold more than 30 days ago.

GitHub integration allows you to maintain your workflows through GitHub, bypassing the trouble of uploading and forking your workflows from BioWorkflows.com. To achieve this, you will need to
  • Integrate your account with GitHub. You can either sign in with your GitHub account, or link your GitHub account with your BioWorkflows account after signing in.
  • Create and maintain your workflows in GitHub repositories
  • When you upload your workflows to BioWorkflows, add the blob URL to "Auto-update from GitHub"
After the workflow is uploaded, pushing changes to your GitHub repositories will automatically update the workflows on BioWorkflows.com. More specifically,
  • If your workflow is in draft mode, the content of the workflow will be replaced by the new version.
  • If your workflow is already published, a new draft version will be created.

Copyright, Licenses, and Others

This depends on the copyright of the license and the license you purchased.
  • If the workflow is not protected by copyright (the seller distributes the workflow under public domain), you are free to revise, redistribute, even resell it.
  • If the workflow is copyrighted by the seller, you can only use it by yourself. unless
  • If you created a team account and purchased the workflow under an extended volume license, you are free to share the workflows with members of your teams

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