journal for entropy landscape (to do for aging landscape)

 science advance

gene ontology dowload, slim versus obo

 

OBO versus Slim

there are confusion yeast subset, GOSLIm (is the a subset of yeast GO or full-genome coverage). Guo think Goslim is a partial coverage of the yeast genome. The http://geneontology.org/docs/go-subset-guide/ seem to suggest that yeast genome-GO is call "slim". 

It seems OBO is a human readable format. 

http://geneontology.org/docs/go-subset-guide/

http://geneontology.org/docs/download-ontology/#subsets

Ghafari suggests: 

https://sites.google.com/view/yeastgenome-help/useful-sgd-links?authuser=0  which linked to a FTP site at sgd:  http://sgd-archive.yeastgenome.org/. and https://downloads.yeastgenome.org/latest/sgd.gaf.gz 

Guo confirmed that *gaf file is what he used. 

GAF format is at 

http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/

But, GAF files is gene-2-GO mapping. Not the GO_tree. 

It seems JASON files contain 'graph', 'node' in its structure. 

https://ontobio.readthedocs.io/en/latest/notebooks.html

Jupyternoteook https://github.com/biolink/ontobio 

TODO: read graph based DNN to see how graph is converted to connection of layers. 

Guo suggests GO-CAM, a nature comment with download link

http://current.geneontology.org/products/ttl/index.html

twitter location

 

twitter profile location 

https://developer.twitter.com/en/docs/tutorials/filtering-tweets-by-location

python genbank parsers

 

https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/genbank/

autograder, codeHS

 autograder

https://readwritecode.blog/these-are-the-autograders-you-ve-been-looking-for-bda0fa8fd8a

GRFP deadlines 2021

important days

https://www.nsfgrfp.org/applicants/important_dates

life science Oct 19

computer science Oct 20

3 Letters, October 30 

parrots lifespan and genomes

Kakapo, lifespan 95 years

Parrots, also known as psittacines /ˈsɪtəsaɪnz/,^[1][2] are birds of the roughly 393 species in 92 genera comprising the order Psittaciformes, found mostly in tropical and subtropical regions.

https://en.wikipedia.org/wiki/Parrot

https://eol.org/pages/1591

https://en.wikipedia.org/wiki/Genomic_evolution_of_birds

https://b10k.genomics.cn/species.html

https://academic.oup.com/gigascience/pages/avian_genomes_collection

biology student researcher advertisment

 Biology/Biochemistry major needed for a gene network + deep learning research project on longevity modeling and prediction

I am looking for an undergraduate biology/biochemistry major interested in teaming up with computer science students to work on using deep learning to model gene networks and lifespan of cells. A relevant publication is “Using deep learning to model the hierarchical structure and function of a cell”, Nature Methods, 2018, https://www.nature.com/articles/nmeth.4627.

Relevant knowledge of the biology/biochem student may include a good understanding of the molecular mechanisms of genetic materials, replication, gene expression, protein biosynthesis and function, metabolism, cellular organization. Most importantly, this student researcher should be eager to learn new concepts and skills. The biology student is expected to work on the molecular biology aspect of this inter-disciplinary project, and receive hourly pay.  Computational skill is not required for this biology/biochem student, but we hope he/she is willing to learn computational skills. 

If interested, please send your resume and unofficial transcripts to xxx@utc.edu

pytorch transfer learning turtorial

 

https://pytorch.org/tutorials/beginner/transfer_learning_tutorial.html

Microsoft Research Ada Lovelace Fellowship

 

Nominations are now open for the 2021 Microsoft Research Ada Lovelace Fellowship and Microsoft Research PhD Fellowship. Doctoral students must be nominated by the department chair’s office in their field of study by August 14, 2020. Students will then be contacted to submit their proposals by September 21, 2020.   The Microsoft Research Ada Lovelace Fellowship aims to increase the pipeline of diverse talent receiving advanced degrees in computing-related fields by providing a research funding opportunity for doctoral students who are underrepresented in the field of computing. This includes those who self-identify as a woman, African American, Black, Hispanic, Latinx, American Indian, Alaska Native, Native Hawaiian, Pacific Islander, person with a disability, and/or LGBTQI+. The award for second year PhD students covers tuition and fees for three years and a $42,000 USD stipend annually.   The Microsoft Research PhD Fellowship is for third year doctoral students also attending a university in the United States, Canada, or Mexico who are conducting research in computing-related fields. The award covers tuition and fees for two years and includes an annual $42,000 USD stipend.   For both awards, students’ research must be closely related to the general research areas carried out by researchers at Microsoft. In addition to the funding mentioned above, Microsoft Research will host a two-day workshop next fall where fellows will meet with Microsoft researchers and other top students to share their research in person and/or virtually as local and national health and safety guidance advises.   You can read more about the fellowships and find nomination instructions at https://aka.ms/ada-lovelace-fellowship-arap and https://aka.ms/phd-fellowship-arap. You may also consider sharing this information via social media:             Ada Lovelace Fellowship - Twitter, Facebook and Instagram             PhD Fellowship - Twitter, Facebook and Instagram   We hope you will help us spread the word about these fellowships! We encourage you to share this announcement directly with your students and department chair’s office, on social media, and/or via topically relevant email lists.   For questions, please contact Microsoft Research Fellowships msfellow@microsoft.com.   For more information on all of our academic programs, visit https://aka.ms/academic-programs-arap.   Thank you,

 

Gonzalo Ramos Chair, MSR Ada Lovelace Fellowship Principal Researcher, Microsoft Research

Neel Joshi Chair, MSR PhD Fellowship Principal Researcher, Microsoft Research

 

 

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cyber career pathway tool

https://niccs.us-cert.gov/workforce-development/cyber-career-pathways