Could a gene network for gliomas be created?
Building_gene_networks_visualizer_P53
Building_gene_networks_visualizer
http://www.ncbi.nlm.nih.gov/pubmed/22203689
http://www.coremine.com/medical/#search?ids=47821&tt=8191&org=hs&t=TERM&i=47821
We are using http://processing.org a free software package from MIT to develop curriculum for students in high school.
Students can explore a cell phone social network and then modify it to represent a gene network for cancer.
http://alignedleft.com/work/relationship-visualizer/
This tool can also be used to create breast cancer gene networks.
See attached Building_gene_network_visualizer.doc for a model of BRCA1.
See Building_gene_network_visualizer_p53.doc for a model of P53.
Try building a C90 gene model in processing?http://www.ncbi.nlm.nih.gov/pubmed/22203689
The greatest challenge the next generation must solve is how to treat cancer with computers to save national and state budgets from health care costs.
I work with NM college interns training them in computer science. This past summer we had CS students from NM Highlands, NMTech, UNM work at DOIT building software for NM state agencies. I worked in AIDS research with USAID in Peace Corps and Los Alamos National Laboratory. I also completed a thesis on mapping the Human Genome and Genbank.
I see state budgets transforming from a K-12 education dominated model to a Medicaid dominated model. Cancer is the fastest growing health cost in medicare and medicaid.
Medicaid Surpasses K-12 Spending in US State Budgets
http://www.decisionsonevidence.com/2012/01/for-state-budgets-medicaid-surpasses-k-12-spending/
Could you develop a game/gene network modeling tool for cancer for students?
Could students use this tool to build bioinformatics programming skills?
http://rosalind.info/about/
http://fold.it/portal/
Recent work at Salk is leading the way to tumor understanding.
This woman is revolutionizing cancer research.
The video in the article shows cells preparing to become cancerous. Could an immune response be generated to polymers that turn off tumor suppressor genes?
http://medicalxpress.com/news/2012-10-cold-viruses-cancer-therapies.html
Could a 3D tool or game be created to help students explore this work?
Blender uses python to display 3D models.
We use Blender to model server rooms in 3D with interns.
Interns learn python scripting.
http://wiki.blender.org/index.php/Doc:2.6/Manual/Extensions/Python
EPMV is a tool for Blender to model molecules. I used EPMV at LANL HIV genome project. How can we develop a beginners curriculum? In Spanish and Portugese?
http://epmv.scripps.edu/download-install-free/perhost
Build a Molecular Game in Blender
Similar to mesh networks, tumors orchestrate gene networks to their advantage.
Mesh networks were used in Arab Spring to redirect packets around ISP’s.
Cancer essentially does the same process by using redundant gene networks to mutate.
FAQs
By comparing gene networks and computer networks students learn valuable skills.
How could we build a cancer curriculum for high school students?
Could they understand the threat cancer poses to medicaid and medicare?
The US Southwest has several cancer challenges you may be able to help with.
BRCA1 in Hispano Women threatens families in the Americas.
The “Wandering Gene and the Indian Princess” book documents the epidemic of cancer in some Hispano families in NM and CO. What are their risks in all the Americas?
http://www.smithsonianmag.com/science-nature/san-luis-valley.html
http://www.amazon.com/The-Wandering-Gene-Indian-Princess/dp/0393081915
STEM projects for minority women need assistance in building STEM programs for minority women. Black women face triple negative breast cancer.
http://www.ngcproject.org/
Women are now being saved from breast cancer using treatments based on tumor biopsies. White women were used to develop the tests. Triple negative breast cancer and BRCA1 plague minority women.http://www.obgynnews.com/conferences/conference-coverage/single-article/0cbfc92dc4ae9d207e6c6d11da7075c7.html?tx_ttnews%5Btt_news%5D=94014
Could analyzing gene networks of tumor biopsies predict cancer outcomes?
Oncotype DX now does this for Estrogen, Progesterone, and Herceptin positive cancer.
Could you build a model for use with triple negative cancer? Notch1 gene? Family ancestry?
http://www.ncbi.nlm.nih.gov/pubmed/21679465
http://www.pubgene.org/tools/Network/Subset.cgi?terms=Notch1
IBM Watson, a medical expert system, may be able to reduce health care costs in the US by building gene networks and improving gene understanding.
Can US students study this health care expert system?
Can they save US medical costs from skyrocketing as people age by diagnosing cancer early?
The US public education budget is now being cut by Medicaid cancer costs.
Cancer is the fastest growing cost in Medicaid/Medicare.
Changes in cancer diagnostics may reverse this trend.IBM is now building a Watson for Cancer at Sloan-Kettering Hospital to reduce health care costs.
New breast cancer tumor diagnostics reduce costs and create an opportunity for IBM to provide the genome community with Watson as a solution to tumor diagnostics data.
The Oncotype DX test of Genomic Health (Redwood City, CA) was approved by Medicare 6/2010. Oncotype uses tumor biopsy databases to cut breast cancer costs.
http://www.genomichealth.com/
http://www.physorg.com/news/2012-03-ibm-nyc-hospital-watson-supercomputer.html
http://www.time.com/time/business/article/0,8599,2049826,00.html
National budgets around the world are now being reallocated to handle the fastest growing budget item, health. Cancer care is the fastest growing disease in health care budgets.
http://www.msnbc.msn.com/id/44671951/ns/health-cancer/t/cancer-costs-becoming-unsustainable-many-countries/
http://www.nih.gov/news/health/jan2011/nci-12.htm
“Medical expenditures for cancer in the year 2020 are projected to reach at least $158 billion (in 2010 dollars) an increase of 27 percent over 2010, according to a National Institutes of Health analysis, a 5 percent annual increase.”
My main interest is to facilitate the early detection of cancer, with low false positives, to reduce the Medicare burden that cancer now poses in the US. Medicaid is now the single largest budget item in state budgets in the US. Cancer care is the fastest growing cost in Medicaid and Medicare.
“Spending on cancer drugs has risen faster than spending in many other areas of healthcare in the United States.”
Medicare Unable to Control Rising Costs of Cancer Care
http://www.medscape.com/viewarticle/587974
The public education budget in the US is now being cut by cancer costs.
Medicaid Surpasses K-12 Spending in US State Budgets
http://www.decisionsonevidence.com/2012/01/for-state-budgets-medicaid-surpasses-k-12-spending/
Could US students project what portion of the national budget will be health care and cancer?
https://www.cms.gov/nationalhealthexpenddata/downloads/proj2008.pdf
What would future medical systems look like with Watson matching therapy per patient?
IBM may be able to implement a Genomic Health like diagnositic to predict cancer?
Would this technology become the single largest money saver in the health system?
How will health insurers and state budgets justify Watson?
How do we define Watson health care savings when it can be used for cancer diagnostics?
Would a future health care system connect many Watsons to interconnect the world’s health systems?
To personalize medicine?
Global Health Profiler cartoon example:
http://scratch.mit.edu/projects/GeneMachine/389166
Could Facebook be used for Watson to match donors?
I did my thesis at the Human Genome Project developing sequence technology and computer algorithms.
I built a Mycin like expert system to assemble genomes. Mycin was originally created for blood diagnostics.
http://en.wikipedia.org/wiki/Mycin
Watson diagnostics are based on Mycin.
Could IBM Watson lead to a Forever Fix?
http://us.macmillan.com/theforeverfix/RickiLewis
How will Watson deal with a DNA superspreader based cancer model?
There is no one cancer but a myriad of derivatives. Curing a moving target?
I saw this working on HIV at Los Alamos. HIV changes, fooling the immune system.
Cancer evolves as it develops and changes context just as HIV does.
http://www.sciencedaily.com/releases/2012/04/120423153138.htm
http://medicalxpress.com/news/2012-05-tumor-cells-equal-reveals-huge.html
http://en.wikipedia.org/wiki/Somatic_evolution_in_cancer
Will Big Data fail to catch cancer?
Can we afford to fail matching cancer to treatments?
http://www.fastcompany.com/1811441/why-big-data-won-t-make-you-smart-rich-or-pretty
Could US students build an IBM Watson? Could INL/Cal Tech create an IBM Watson gene network toolkit?
https://www.ibm.com/developerworks/mydeveloperworks/blogs/InsideSystemStorage/entry/ibm_watson_how_to_build_your_own_watson_jr_in_your_basement7?lang=en
Molecular detection of Breast Cancer – A new technology changes treatment
http://www.cancerworld.org/pdf/1233_06_13_cw12_coverstory.pdf
http://www.nature.com/nature/journal/v415/n6871/abs/415530a.html
http://gcat.davidson.edu/Pirelli/index.htm
http://www.nejm.org/doi/full/10.1056/NEJMra042342
http://www.ncbi.nlm.nih.gov/pubmed/12233926?dopt=Citation
http://compbio.cs.umn.edu/Papers/DMBI_TaeHyun.pdf
http://www.biomedcentral.com/1471-2164/7/278/
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0002994
Rosetta Uses MathWorks Tools to Predict the Clinical Outcome of Breast Cancer Patients
http://www.mathworks.com/company/user_stories/Rosetta-Uses-MathWorks-Tools-to-Predict-the-Clinical-Outcome-of-Breast-Cancer-Patients.html
http://www.mathworks.com/tagteam/7790_91069v00_Rosetta_story.pdf
PAM may allow women to diagnose themselves at home using home computers to compare images from month to month.
Screening for Breast Cancer Without X-Rays: Lasers and Sound Merge in Promising Diagnostic Technique
http://www.sciencedaily.com/releases/2012/05/120507141351.htm
How will breast cancer survivors embrace this technology?
Will this allow the cost of digital mammograms to decrease?
Will women choose this option?
Will PAM allow women to diagnose themselves at home using home computers to compare images from month to month?
How will breast cancer survivors embrace this technology?
Will this allow the cost of digital mammograms to decrease?
Will women choose this option?
I created a similar image analysis tool at LANL for gene sequencing.
http://www.mathworks.com/products/image/
Will we all use this system for medical diagnosis?
Will computer speed increase?
How will US Budget benefit?
Will we all have this expert system on a home PC?
Can US women develop a new paradigm for cancer treatment based on family heritage?
Many women in the Americas are at risk due to their Jewish heritage. Many are unaware of the risks.
The clinical profile of breast cancer of ethnic groups, can be defined by a founder effect, in Israel 51% were Ashkenazi Jews (AJ), 26% were Sephardic Jews (SJ).
http://www.ncbi.nlm.nih.gov/pubmed/15219486
http://www.bjpa.org/Publications/details.cfm?PublicationID=7178
Many Hispanic Americans have Sephardic roots. Many do not know their risk for cancer.
http://www.smithsonianmag.com/science-nature/san-luis-valley.html
http://www.4sephardim.com/
http://www.nytimes.com/2005/10/29/national/29religion.html
For instance, the Rev. William Sanchez, 52, a Catholic priest in Albuquerque, spent years researching his family’s past in New Mexico before a DNA test three years ago showed that he almost certainly had the Jewish Cohanim marker.
Since then, Father Sanchez has sought to educate his parishioners on the connections between Catholicism and Judaism, and has helped oversee the Nuevo Mexico Project, which tries to identify Sephardic ancestry among Hispanics from New Mexico. He has encouraged more than 100 of his parishioners to take DNA tests.
Father Sanchez has also introduced some Jewish customs at St. Edwins Church in Albuquerque, where he serves; he blew the shofar, or ram’s horn, this month during the Yom Kippur holiday. At another parish where he used to work in rural northeastern New Mexico, in the village of Villanueva, he would hold an annual Passover supper.
http://articles.latimes.com/2004/dec/05/nation/na-heritage5/2
http://www.familytreedna.com/public/NuevoMexico
Could US build a model Sephardic family phylogenetic tree for students to learn their cancer risks?
US needs health care workers trained in genetics.
Global Neural Network Cloud Service for Breast Cancer
http://www.google.com/intl/en/events/sciencefair/projects/gsf83.html
I have given lectures on Comparative Genomics in Cancer for high school students.
Having 3D computer games or a GUI for student use would be helpful.
We use http://blender.org to build 3D animations using python scripts.
A gene network modeling tool based on Sophia could help students visualize cancer.
Could Watson for Cancer at Sloan Kettering use it to evaluate cancer tumors?
The 3D Sophia network GUI is impressive. But could it model the P53 gene? Videos show a complex network.
https://sophiahome.inl.gov/
Cal Tech is developing embryonic gene expression maps.
http://www.its.caltech.edu/~mirsky/
http://www.sciencedaily.com/releases/2012/08/120829092145.htm
I worked with AIDS patients and their children as a Peace Corps Volunteer.
I did my thesis on Computer Assisted Genetic Mapping at the Los Alamos Human Genome project. I built bioinformatics software used by Human Genome Project.
