spBRAINghetti

I [the founder] have been keeping hand-written notes on all things neuroscience for ~20 years. (In olden days this was record-keeping of all things "biological psychology.") As my research focus became more molecular biology based, these notes evolved into ≥ 50 % gene findings. Additionally, the origin of CMK Data is laboratories offering up "analyzed" bioinformatic data and asking "What do I do with this? Can you help?" "What does this mean?"
A few things became clear from looking at these datasets across neuroscience-related diseases:

• "Analyzed" data is anything but. Rather, it is processed data, which is not ideal for publication on its own.
• Genes repeatedly appear across neurodegenerative, neurodevelopmental, and acute neuronal injury conditions. Annotation databases link to housekeeping biochemical processes or molecular function. My current hypothesis is that these are more neuroscience-related than disease-related, however there are no annotations for either, so this can't be determined.
• A single brain is just not computationally capable of detecting the patterns needed to uncover neuroscience-specific annotations. There needs to be a central repository of notes and research as well as scientists across diseases looking at the information.

On the whole, something like spBRAINghetti has been a long time coming in my work and a long time needed in general. CMK Data has the resources to make this a reality, primarily obsessiveness in accuracy and the need to be thorough.

There is none.   We are monetarily poor but intellectually motivated. Our moms and dads buy us soda and pizza sometimes.

• Suite of analysis tools using custom annotation databases
• Non-coding RNA repository
• NLP-based extraction of data (everything is manual currently, which is the correct way to start)
• Migration from HTML-only presentation (the reason spBRAINghetti appears this way is part strategic (for early launches) and part ease of management)
• Orphan disease integration
• Publication-ready visualization tools
• Possibly report generation (this can devolve into not looking up original research, so needs to be handled with stewardship and is not definitively planned)
• User feedback infrastructure (you will be able to toggle it off)

On the last point: The main goal of this site is a central repository that is neuroscience-specific. As important as peer-reviewed publications are, researcher input is valuable if handled correctly. Especially when someone is looking at their own past research. I would like to foster this type of interaction to allow senior scientists to comment on patterns they have found that are not published or were not known at the time of their previous data viewing. While there are specific plans to incorporate this, it probably will not come out until a late, late iteration.

I usually forget to spell-check. Sorry.
In addition to a valuable resource, I aimed to make a site that is interesting upon first visit and usable with minimum fumbling. There are unorthodox elements, such as my love of random buttons, but these elements actually have a purpose beyond creative expression. There are a few key hurdles to proper data presentation in bioinformatics:

• Maximizing information dispersal without a busy design
• Keeping the readers' interest long enough for them to orient to the material
• Human memory. Creating something that can be engraved on the viewer's memory so they can later recall such as "I think I saw this here, I will go back and look."

The last point is the main reason I do not use movable maps. Most data presentations are flat by design.

For the most part, spBRAINghetti encourages reading and citing original research.

However if this was a super useful resource and you want to help spread the word:
Use the website as a reference in the format needed:
NLM

APA

spBRAINghetti is coded/scripted in Python and JavaScript with HTML and CSS formatting. All code is original and structure may deviate from formal rule prescriptions. There is no formal database structure or download/export option. The pages you are viewing likely end in html. There are a few reasons this is done at this point in development. It will change as the site gains traction.

It's just me. I pretend I'm a team. Don't tell. I We never will.