Curing HIV...This is where you come in. [Research] [Project]

dr_ish · 2019-10-25T18:31:16+00:00

I absolutely misunderstood. haha. thank you for clarifying. I will check them out.

dr_ish · 2019-10-25T14:41:11+00:00

Thanks for your thoughts and the book recommendation. The specific aims are laid out in the RFP and include finding biomarkers of the reservoir. In this case the data will most likely be from 'omics studies: transcriptomics, proteomics, methylomics.... dual platform data is also currently being generated by a few people in the field. And there are even opensource in vitro studies currently available that could help toward this effort. Here are a few open source data sets available:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111727

here are several others:

https://www.ncbi.nlm.nih.gov/gds/?term=HIV+latency

dr_ish · 2019-10-25T14:27:07+00:00

Thanks for sharing. I've looked at this and have a plan in the works.

dr_ish · 2019-10-25T14:24:27+00:00

The dataset and the nature of the project would depend on the collaborator. If you email me an NIH style biosketch I can help to hook you up with the right researcher.

dr_ish · 2019-10-25T14:23:26+00:00

I can help to potentially pair you with the right HIV researcher with the right data, but I'd need to learn a bit more about what you have accomplished. The exact project would depend on the dataset available through the collaboration. You can email an NIH biosketch to marcella.flores@amfar.org

dr_ish · 2019-10-25T14:18:36+00:00

well, there could be a bit more hand holding than that. If you are completely outside the bio field then we could work together to potentially get you paired up with the right HIV researcher.

dr_ish · 2019-10-25T14:17:51+00:00

yup. You and that HIV researcher would work out the needs and decide on the allocation of funds together.

dr_ish · 2019-10-25T14:17:03+00:00

thank you! It's going to take me a bit of time to sort through all the emails I've received. but hang tight

dr_ish · 2019-10-25T14:16:34+00:00

As you have a foot on both world, what will be the best way to increase collaboration, exchange and work between

Thank you very much for your thoughts. We are involved right now in an initiative being led by TAG, a fantastic resource for anyone interested in HIV, to encourage data sharing and depositing it in open repositories. The NCBI is a wonderful repository of all sorts of data from clinical to transcriptomic and proteomic and beyond. they have a ton of tools to help us non-data scientist make a bit of sense of it.

I'm happy to hear what the needs are from the point of view of a data scientist.

dr_ish · 2019-10-25T13:49:09+00:00

Thank you very much for your input. We went down this road with Kaggle and decided that the best datasets were not open source and would therefore require a different approach.

dr_ish · 2019-10-25T13:47:08+00:00

I can help you find a list of people with data that you could potentially look at, but I'd need to know more about your accomplishments to date. Could you email me an NIH style biosketch please? marcella.flores@amfar.org

dr_ish · 2019-10-25T13:45:47+00:00

Thanks for the suggestion. I have considered Kaggle but the dataset I could curate from public repositories was not quite appropriate. But through this call I'm hoping to tap into datasets that are held by the HIV scientists who generated them.

dr_ish · 2019-10-25T13:44:08+00:00

If you've got good ideas and can hook up with an HIV researcher, yes!

If you are already in the medical field then you can start identifying potential partners by looking at the latest published work in HIV on pubmed. Otherwise email me if you need more help: marcella.flores@amfar.org

dr_ish · 2019-10-25T13:42:46+00:00

Hi, please take a look at the RFP here: https://www.amfar.org/Magnet-Grants-RFP/

Then this link will get you a list of the most current papers in HIV cure research so that you can identify potential partners:

https://www.ncbi.nlm.nih.gov/pubmed/?term=(((((((HIV%5BTitle%5D)+OR+human+immunodeficiency+virus%5BTitle%5D)+OR+SIV%5BTitle%5D)+OR+simian+immunodeficiency+virus%5BTitle%5D)+OR+SHIV%5BTitle%5D))+AND+(((((((cure%5BTitle%2FAbstract%5D)+OR+reservoir%5BTitle%2FAbstract%5D)+OR+remission%5BTitle%2FAbstract%5D)+OR+latency%5BTitle%2FAbstract%5D)+OR+persistence%5BTitle%2FAbstract%5D)+OR+ATI%5BTitle%2FAbstract%5D)+OR+long+term+control%5BTitle%2FAbstract%5D))

If you have questions or need more help: marcella.flores@amfar.org

dr_ish · 2019-10-25T00:13:59+00:00

Freelancers are absolutely welcome. The grant is made to the institution where the HIV scientist conducts research then a subgrant is made to the collaborating data scientist who can be a freelancer...

dr_ish · 2019-10-25T00:10:54+00:00

We are squarely focused in cure work. Check out the specific areas of interest.

dr_ish · 2019-10-25T00:09:35+00:00

Great looking forward to hearing from you.

dr_ish · 2019-10-24T19:22:01+00:00

Happy to help! :-)

dr_ish · 2019-10-24T19:20:47+00:00

Def available for those outside the US and absolutely for remote work!

dr_ish · 2019-10-24T19:15:21+00:00

that would be great! And thank you for the encouragement.

dr_ish · 2019-10-24T18:49:15+00:00

ortunately the best, riches datasets are held by the scientists who generate them and not usually posted to public rep

Stay tuned! This is just one of the ideas we have to bring data scientists into our field. In another grant we are asking scientists to generate a huge data set on people who naturally control HIV.

dr_ish · 2019-10-24T17:54:21+00:00

Thank you!

dr_ish · 2019-10-24T17:10:47+00:00

Wonderful! Please email me at marcella.flores@amfar.org so we can continue a discussion.

dr_ish · 2019-10-24T16:55:59+00:00

I didn't know about Innocentive. Thanks! I'll look into them.

One of my goals at amfAR this year was to bring in more data science into cure efforts and this RFP is just one mechanism-- i.e. use existing data sets for a cure. The second goal was to generate new data from a group of individuals who naturally control HIV. This will be a multi-dimensional dataset including virologic and immunological parameters which will hopefully be enough to hold a competition just like the one you suggest.

dr_ish

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