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Author Topic: zRMicroArray - phase 2 - Gene Expression Analysis software  (Read 4556 times)
equipoise
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January 21, 2015, 07:02:42 PM
Last edit: October 04, 2016, 11:29:41 AM by equipoise
 #1

zRMicroArray software implements all of the functionalities, needed for preprocessing and statistically analyzing single-color cDNA microarray data. It allows for parallel execution of the implemented algorithms which makes it appropriate for multiprocessor and multi-core computer systems. The Graphical User Interface (GUI) is easy and intuitive to use, which makes it particularly suitable for users, who do not have specialized programming or statistical background. The software is free for noncommercial use and it allows scientific laboratories, institutes, universities, students, etc. to reduce their budget on expensive software and concentrate it on research and experiments.
The current version of the software is successfully used in some US Universities labs and by many students. It’s used to analyze the data for some scientific publication like this one: Dietary fish oil and curcumin combine to modulate colonic cytokinetics and gene expression in dextran sodium sulphate-treated mice. I added some additional useful functionality based on feedback from the users, but it’s now the time to bring it one step forward. A new and rewritten version should be done to add additional useful tools and functionalities like support for two-color microarrays and Next-Generation data analysis. This will take substantial amount of resources and those should be evaluated.

EDIT: White paper added: http://zrmicroarray.com/white-paper/

zRMicroArray phase two goals:
1) To analyze five years of feedback from the real world users and sketch the new functionalities to be implemented.
2) To communicate back the new functionality to the researchers who used the software in the past and to analyze their new feedback.
3) To create a basic design of the new version and evaluate the development time needed.
You could find more information about the project on my blog and on zRMicroArray.com (currently under development). Phase two of the project will take about three months and I don’t have the resources to fund it myself. Your donation could help to find a cure or a better and cheaper diagnostics for a disease, and could lead to better understanding of the underlying regulatory mechanisms of the living cell. Donation to this project is of your own free will and you are not buying any product or service by donating.

Inspirational video: The Inner Life of the Cell (Harvard University) (watch it with sound)

Thank you!

Bitcoin donations:
Code:
1KzJr9xkwmY4ioN5wGTGJsT4Q7pLKABph1
Monero donations (XMR):
Send to zRMicroArray.com, ChangeTheWorldWork.com (OpenAlias) or to the following address:
Code:
4AUoJ141b18EbZBAqmVq1cZSR2mVYtH1VaTsALSiMqAMFHbT38SwD3UPy5vUtmu3QL9hpR8RFFMPwfBcZzwEwqdV58yejWS
BURST donations:
regular donations:
Code:
BURST-GFWT-LEP4-Q592-62JQZ
AT crowdfunding donations (you'll get your BURST back automatically if the goal amount is not reached in 6 weeks):
Creator address:
Code:
BURST-RUL4-HV8X-C2US-79AAU
AT owned address: (send to this one for the AT if you are not using additional "atcrowdfund.html" file added to your BURST wallet)
Code:
BURST-P8C8-4N7P-2L5E-CXYYH
Litecoin donations (LTC): -- no donations till now --
Code:
LgyDsxSqcEaneMeqj6gqCDVDb8zqD4dWXh
Darkcoin donations (DRK): -- no donations till now --
Code:
Xw7pxQDmfxVY8m1m1kZq1HYv3947G7CETa

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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equipoise
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February 05, 2015, 12:40:53 PM
 #2

A screenshot of the current zRMicroArray version:


About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 11, 2015, 08:45:52 AM
 #3

Automated BURST crowdfunding transaction deployed. The AT should return you back all the BURST you donate (except ~7 burst fee) if the project goal of 1000000 BURST is not reached in 6 weeks. 1000000 BURST won't be enough (~400$ at the current price), but it would be a start. Donations (if any) will be converted to XMR and kept there until a substantial amount is reached.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 12, 2015, 07:57:04 PM
 #4

Crosspost:
I finally managed to deploy a crowdfunding AT for my project at BURST-RUL4-HV8X-C2US-79AAU:
Quote
zRMicroArray is a gene expression analysis software, which implements all of the functionalities, needed for preprocessing and statistically analyzing single-color cDNA microarray data. The software is free for noncommercial use and it allows scientific laboratories, institutes, universities, students, etc. to reduce their budget on expensive software and concentrate it on research and experiments. The current fully working version should be rewritten based on 5 years of user experience and feedback. Support for Next Generation Sequencing data should be implemented and additional graphical representations of the data and results would contribute big to the software. Donations will help to make zRMicroArray a viable tool for a researcher to find a cure or a better and cheaper diagnostics for a disease, and could lead to better understanding of the underlying regulatory mechanisms of the living cell. Details: https://bitcointalk.org/index.php?topic=932075.0
Project details: zRMicroArray (bitcointalk)
Inspirational video: The Inner Life of the Cell (Harvard University) (watch it with sound)

Looks like a very interesting project.. probably won't be participating due to this clause though:
"Donations (if any) will be converted to XMR and kept there until a substantial amount is reached."

Btw, would be nice if you had a goal that you actually needed to reach somewhere, so we knew how much you actually needed and how realistic it would be to raise that much.
For the phase 2 of the project as defined in the zRMicroArray - phase 2 goals (bitcointalk) involves some consulting with professors, PhD students and researches. That's a lot of communication with different teams currently using the software in order to sketch the design of the new version. I suppose most of them will be responsive and will be willing to help, but maybe I'll need some payed consultations here ant there. My approximation of the funds needed for phase 2 of the project is anything between 5000$ and 9000$. Phase 3 of the project will involve the actual implementations - a lot of statistical/bioinformatics packages are already there to use and open-source, but the NGS problems for different platforms/methods/genomes could be a huge development/research/experiments effort. At the end of phase 2 I'll have a good approximation for phase 3 funds needed, I hope. For phase 3 I'll definitely need at least one more developer. If the approximation for phase 3 is way too high, then my intention is to first try to optimize it and try to get funds to implement those things, which will take less effort, but are still valuable to the project. The current fully functional version took me 8 months to develop (without a single dollar of funding), and the next version would definitely take more at least an year. I know of a commercial tool with almost the same functionality as the current zRMicroArray version, which took a team of 3 people two years to develop. I know that this sentence "Donations (if any) will be converted to XMR and kept there until a substantial amount is reached." could withhold some support for the project, but that's what I intent to do and I believe it's the right thing to state it now. So many IPO/ICO/shitcoin obvious scams collected tens of millions in funds, but I'm not sure it's realistic to raise any funds for such a bioinformatics project in the current bear state of cryptocurrencies at general; however, I can't fund the project on my own so I'm willing to try crowdfunding it.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 13, 2015, 11:07:23 PM
 #5

Have donated a small amount via BURST. Best of luck.

curious stuff from the world of cryptocurrencies: http://cryptolonography.tumblr.com/
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February 14, 2015, 06:35:56 AM
 #6

Thank you!

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 17, 2015, 01:01:36 PM
 #7

I just got a 300000 burst donation ($ 118.57 at the current price). Thank you very much!
The first zRMicroArray BURST AT crowdfunding case is now 30.56% funded:

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 17, 2015, 06:02:18 PM
 #8

Crosspost:
...
I have another greater project, I and a team of four worked on during the last 12 years. It's a non-invasive health diagnostics tool which gives information about the working of 12 internal human organs and systems. It could early diagnose functional organ deviations before they are clinical. It could diagnose some diseases like diabetes and prostatitis for example and even catch some life threatened emergencies before they occur and would suggest the patient to immediately go to a specific medical examination. It could for example tell if a patient was a sportsman and what kind of sports he trained (heavy sports, fast sports, etc...). In those 12 years we measured 5000+ patients and we trained an artificial neural network to find cases/similarities based on those patients. We've passed the proof of concept phase and we are now ready to bring it to a larger scale - give a non-commercial licences to some physicians and teach them to use it. They could then diagnose their friends/family/patients and compare it to their clinical diagnoses/tests/examinations to proof it's working. With more data collected we could calibrate the devices/software even better and find more relations in the data. The tool have the potential to make the health diagnostics much cheaper and with it's automatic diagnostics mode it could bring diagnostics to places were it was never available even without a physician. The project require small amount of funds to produce the devices, teach the physicians, install and configure the software, etc. I approximate the funds needed to bring it to 5 physicians in this early phase to about 8000-10000 $, and if the project scales a lot it would become much less. I have to talk with the other team members about crowdfunding and cryptocurrencies at general and get their approval to create a crowdfunding case for this project. Our leading scientist is 78 years old physicist. I think he'll get the cryptocurrencies and crowdfunding ideas and what this could bring to the future generations. I hope I could use the zRMicroArray funding AT case(s) as a proof of concept to him that cryptocurrencies crowdfunding could bring some funds to a scientific project if the funds needed are small enough. Thank you all who donated so far! Special thanks to the guy who donated 300k!

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 18, 2015, 03:38:02 PM
 #9

I like your ambitious projects .

Personally , I do support medical research . I might talk soon about your software to people I know well , they work in related fields at top
institutions as MD and Researchers , and also as Peer-Reviewers . I need to know a bit more and make still my mind up for a good parlay . 

BURST AT's is a great way to innovate in the crowdfunding scenery . Consider keeping donations in its denomination to honour their work . This is desirable , just , and needed .

Please add also XDN , DarkNotes , to your list of options . I will donate in BURST & XDN under the condition that they are also honoured . By doing the right thing you might well be safer longterm , as XMR remains on a looong sell-off , the other options have much less possible downside , more large upside potential or a clearly positive growth trend from the bottom up which could only  give you an additional boost instead of the existing risk of dwindling funds — as soon as their appreciation and adoption consolidates .

That said , do as you wish , I am looking forward to a positive outcome for your project and for all of us . All the Best ! Keep it coming .

I bookmarked the link to this project to check back regularly and see what's on the table …
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February 18, 2015, 06:07:49 PM
 #10

^Did you mean DuckNotes? I currently don't intend to add those.
>Consider keeping donations in its denomination to honour their work
=Selling it means that more people could get it and it's spread trough a bigger community, more volume, less pumps and dumps, etc. It should stand 0.5 BTC dump or it's not going anywhere.
>The other options have much less possible downside
=I don't think so. In Monero (XMR) I see a great dev team with a great management of priorities, great community, mathematically proved privacy, not premined, not instamined, no scam. If it succeeds it would be big, if not there is no chance for the others mentioned too. That's just my opinion.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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February 21, 2015, 11:27:45 AM
 #11

Donations till now (current $ price):

Monero: 22 XMR (6.55$)
Burst AT: 308062 BURST pledged out of 1000000, 11637 blocks to go, 30.81% funded (122$) - those will be automatically returned to the sender if the AT funding goal is not reached in ~5 weeks.



About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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March 03, 2015, 02:27:45 AM
 #12

+0.02370471 BTC (~6$) donation from a friend.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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March 04, 2015, 05:03:24 PM
 #13

+10 XMR donation from a few days ago. Thank you!

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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March 23, 2015, 02:57:57 PM
 #14

Crosspost:
Less than 57 hours until my zRMicroArray crowdfunding AT expires. During the previous six weeks it got 32% funded. If you feel like this project matters, please show your support even with a tiny donation. It could be the starting bit of the successful funding of the project. You could send BURST to BURST-P8C8-4N7P-2L5E-CXYYH in order to fund this AT. You could find more details about the project in my signature. Thank you!



About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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March 24, 2015, 11:17:43 AM
 #15

^Now it's 44.56% funded, but just 540 blocks to go until the funds are sent back if not funded.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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March 26, 2015, 02:51:42 PM
 #16

Burst crowdfunding AT was not funded and funds were sent back.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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June 18, 2015, 10:38:19 AM
 #17

Bump. I've just finished working on some two-color microarray analysis to find differential expressed genes for some different experiment designs. It still won't be easy to add two-color microarray functionality in the zRMicroArray workflow, but I hope some day I'll find the time and the resources for the new version. Next few months I'll use some of my free time to work on some next generation platforms analysis which is one of the other functionalities zRMicroArray needs.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
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October 04, 2016, 11:27:25 AM
 #18

Next few months I'll use some of my free time to work on some next generation platforms analysis which is one of the other functionalities zRMicroArray needs.
The day after my previous post, I was beaten almost to death - 9 fractures on the skull, and a fracture of the kneecap. Court cases are still ongoing, I'm still threatened by the same person, who beat me, and I'll have another operation to remove the hardware implanted in my kneecap. That's why the bold part never happened; however, finally, zRMicroArray.com is up and running. You could find the White paper published there.

About me | zRMicroArray - phase 2 - Gene Expression Analysis software | [Weed Like to Talk - Bulgaria] Start a wave of cannabis seminars in Europe | Monero weighted average price stats: moneroprice.i2p
BTC: 1KoCX7TWKVGwqmmFw3CKyUSrKRSStueZar | NMC: NKhYEYpe1Le9MwHrwKsdSm5617J4toVar9 | XMR (Tip me a beer OpenAlias Monero address): tip.changetheworldwork.com
[XMR] Monero - A secure, private, untraceable cryptocurrency: 4AyRmUcxzefB5quumzK3HNE4zmCiGc8vhG6fE1oJpGVyVZF7fvDgSpt3MzgLfQ6Q1719xQhmfkM9Z2u NXgDMqYhjJVmc6KX
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