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FlowRepository-updating-RFP for v2

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mleipold

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Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Mon Oct 28, 2019 2:59 pm

FlowRepository-updating-RFP for v2

Hi all,

Some of you may have already seen this from the Purdue flow listing.

In short: the current status of FlowRepository is problematic, due to technology changes and security concerns. ISAC has *finally* released an official Request For Proposals for FlowRepository version 2.

I have attached the RFP to this post. Please note the current deadline of December 15, 2019.


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"Project Overview
This RFP describes the requirements for a public, online, Cytometry Data Repository (FlowRepository V2). FlowRepository V1 has reached the end of its life. It is built on now outdated technologies that cannot be reliably updated presenting security and stability issues and is hosted on a single server, making it susceptible to failure and presenting remote users with decreased performance.

FlowRepository hosts public flow and mass cytometry data sets used in publications that are linked to online manuscripts through many journals, including Cytometry A (Figure 1). It is critical that these data and journal links are preserved, both because they represent a substantial investment in data generation by many funding agencies, time and effort by PIs and researchers, but also because they contribute towards reproducible science. It currently hosts 147,495 FCS files (1136 GB) from 582 public datasets and 631 that are in the process of being released.

FlowRepository V2 should capture many of the features as well as all the data available in FlowRepository V1, but should leverage robust technologies, including distributed storage and hosting, allowing it to scale to many users and large data sets. Applications are due December 15, 2019. Consideration will be given to FlowRepository V2 proposals that either are ultimately managed by ISAC or by the vendor themselves. The major requirements are described below."

"Evaluation:

The proposal will be evaluated by the ISAC Flow Repository Task Force and ISAC Leadership. Emphasis will be placed on the experience of the respondent and the completeness of the application. The respondent should identify the individual person(s) who will manage the project including their qualifications/experience. The proposed budget will be a major consideration.

Questions about and the Response to this Request for Proposal:
Responses should be mailed/emailed to:
Ryan Brinkman, Ph.D.
Email: rbrinkman@bccrc.ca
Subject line: FlowRepository RFP "
Attachments
ISAC FlowRepository RFP 191026.docx
(225.25 KiB) Downloaded 63 times
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dtelad11

Master

Posts: 107

Joined: Mon Oct 31, 2016 6:26 pm

Post Mon Oct 28, 2019 3:17 pm

Re: FlowRepository-updating-RFP for v2

This is great news! Sounds like they want to scrap the thing and build a whole new system (migrating the old data with it).

I am concerned by three aspects of the applications:

One, December 15, 2019, is just around the corner. A month is not enough time for a serious application; in fact, I am wondering whether they already have a contractor for this and they're just putting the RFP as a formality.

Two, while they are asking for maintenance costs, that is mentioned off-handedly and I am worried they will focus on developing the infrastructure over long-term maintenance.

Three, Brinkman is a brilliant researcher but if I understand the situation correctly he is fully committed to a financial entity (Cytapex) over academic research, and I think that might cause a conflict of interest.

I hope a strong institute or company takes over and builds a new version. However, I am not going to apply (even though Astrolabe already covers 60% of the spec!) due to the concerns above.
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tomaskalina

Participant

Posts: 9

Joined: Fri Dec 20, 2013 9:19 am

Post Mon Oct 28, 2019 5:26 pm

Re: FlowRepository-updating-RFP for v2

Hi all,

we, at ISAC, really want to have Flow Repository up and running as this is important for the field.

To your concerns:
One - short period for RFP, well you might be right, we will see what will be the response. And no, we dont have any contractor.
Two - we spent a lot of discussions on the short term development vs. long term maintenance, I dont think this is ignored at all.
Three - the role of Ryan Brinkman: as you know two people were instrumnetal in creating FR: Ryan Brinkmann and Josef Spidlen. They both work for commercial entities now, which is why we set up the RFP call. We appreciate that Ryan is willing to help ISAC to formalize the RFP. We are definitely sensitive to any potential conflict of interest and we take measures: The RFPs will be evaluated by ISAC's Flow repository Task Force and decisions will be made by the ISAC council.

Saying all above, I do think creating FR v 2 is a challenge for us, the cytometry community and we would really appreciate if the computational cytometrists help us achieving this goal for the benefit of the whole community.

Best regards, Tomas
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dtelad11

Master

Posts: 107

Joined: Mon Oct 31, 2016 6:26 pm

Post Tue Oct 29, 2019 3:00 am

Re: FlowRepository-updating-RFP for v2

Tomas, thank you for the prompt and extensive reply! I'm a believer in FR and I hope the RFP finds the right group to make v2 happen.
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mleipold

Guru

Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Oct 29, 2019 2:58 pm

Re: FlowRepository-updating-RFP for v2

Hi all,

Since my initial posts, I've had some off-Cytoforum discussions with various people about this, and there have been some questions.

Therefore, I would like to clarify that from a forum POV, I strongly encourage any and all who are interested in giving feedback/comments/wishlist items for FRv2 to feel free to post them here. I think it would only strengthen future Proposals if the users of FlowRepository make it clear what they *do* and *don't* like about the current FRv1, and what they would like to see in FRv2.


Mike
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mleipold

Guru

Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Nov 14, 2019 8:27 pm

Re: FlowRepository-updating-RFP for v2

Hi all,

I'll chime in with some initial feedback/comments/wishlist items for FRv2.

1. Larger downloads: the zipping process fails on hundreds of files in a single entry. For example, I tried a dataset that was about 350 files: the upload was fine. However, the download starts to zip, gets a bit over 1GB in size, and then stops.

2. Dataset metrics: number of downloads, etc. This is somewhat done already with the "10 Most Popular Datasets" page: http://flowrepository.org/public_experi ... ons?top=10
But for those of us interested in data use/reuse, it would be nice to have measures of this (or, for the programmers, an API to access it?)

3. Easier file annotation (case, control, etc), rather than one-by-one. At least in my experience with uploads, I throw the files up, then haven't been able to find a way to apply sample information in a batch way. Maybe I'm missing something, but I've only been able to annotate file by file, which is problematic for hundreds of files, and one reason why my entries have poor MiFlowCyt scores.

4. Easier annotation of keywords, funding agencies, affiliations: drop-downs are *NOT* working well. Actually, the dropdowns in general aren't working well. At least on my Mac laptop using Firefox, I have trouble scrolling. And that's even if I feel like trying to scroll through literally hundreds of affiliations. A simple text box would be more useful, IMO.

5. Ability to add an associated reference/PMID *after* public release, if necessary (without involving FR managers). Once a dataset goes Public, any alterations have to go through the admin team, even if it's just to add a PMID to the entry when your paper is finally officially published with page numbers, etc.

6. Ability to upload the same file to more than one FR entry.
- For example, the researchers I worked with for a large Gates study are planning to release a couple papers. The first one will only deal with a subset of the timepoints, so that's all that they want to make public at first. Their second paper will involve the additional timepoints. Yes, we could make two FR entries with each unique subset of files, but since at least the first set will also be included in the analysis, the plan is to release the entire dataset with the second paper.
- I've tried uploading Subset 1, but since I had already uploaded the Entire dataset, FR refused my Subset 1 upload. I assume this is a deliberate Feature rather than a Bug.
- But this could also apply for algorithm papers that reuse only parts of previous datasets. In my experience, exactly which (say) 5 files of the dataset of 25 files were used is *not* well-annotated. However, allowing the algorithm authors to re-upload the files as separate datasets would make that explicit.

7. Alert for new dataset (keyword, author, etc). This is minor, but goes back up to the information scraping/searching: as someone who's trying semi-successfully to keep a running list of CyTOF papers and datasets, having an Alert capability would be appreciated.


I'll add more as I think of them.

Mike

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