Thursday, December 14, 2017

data science tools and machine learning

https://turi.com/learn/userguide/

https://www.coursera.org/learn/ml-foundations/home/welcome

Friday, October 13, 2017

https://www.cscu.cornell.edu/news/statnews/stnews11.pdf

Stat Newsletter of Cornell Uni related stats and methods with tools to use.

Thursday, July 20, 2017

aging journals

 Aging Research
http://www.scimagojr.com/journalsearch.php?q=19600166318&tip=sid&clean=0


Experimental Aging Research

http://www.tandfonline.com/action/authorSubmission?journalCode=uear20&page=instructions

Current Aging Science

http://benthamscience.com/journals/current-aging-science/

Monday, July 17, 2017

linux free course and tutorial

https://courses.edx.org/courses/course-v1:LinuxFoundationX+LFS101x+1T2017/info

GeneOntology Pathway Analysis Tools & Resources

Biological Database Network,Gene Conversion:


https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

biological ID translator:


http://bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html#bitr-biological-id-translator

myGene package in R environment:


reference page
: http://bioconductor.org/packages/release/bioc/html/mygene.html

Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mygene")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mygene")





Tuesday, March 21, 2017

Aging Cell submission guidelines

See: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1474-9726/homepage/ForAuthors.html for more information.

Submission of manuscriptsImportant Note to Authors: submission requirements for Aging Cell have changed. Due to the high volume of papers submitted to the Journal, limits have been imposed on the character count of articles, the number of figures, references, and so forth. Please see details below for specific requirements.
General InformationAging Cell now accepts submissions online at http://mc.manuscriptcentral.com/agingcellAll authors should read and apply the instructions, including specifications of file types for text and illustrations given on the site. Should authors encounter difficulties they may contact the ScholarOne support desk at 434 964 4100 or 888 503 1050 or via E-mail at: ts.mcsupport@thomson.com
Authors who cannot submit their manuscripts online should contact the Managing Editor, Stephanie Waller, Aging Cell, King's College London, James Clerk Maxwell Building, 57 Waterloo Road, London SE1 8WA. E-mailagingcell@kcl.ac.uk.
The Editors-in-Chief will choose a Supervising Editor in an appropriate field of interest to supervise the review of each article. Authors are requested to provide a list of up to five possible reviewers, including, if appropriate (given their areas of expertise), members of the Aging Cell Editorial Board. Papers considered to be outside the field of interest of the Journal will be returned without delay. All questions about the status of manuscripts under review should be directed to the Editorial Office. Please use the e-mail address agingcell@kcl.ac.uk for such enquiries.  Pre-submission enquiries and questions about scientific matters can be addressed to any of the Editors-in-Chief: Peter Adams (p.adams@beatson.gla.ac.uk), Adam Antebi (aantebi@bcm.edu), Ana Maria Cuervo (amcuervo@aecom.yu.edu) or Brian Kennedy (bkennedy@buckinstitute.org).
Papers are accepted on the understanding that no substantial part has been, or will be, published elsewhere.
The journal to which you are submitting your manuscript employs a plagiarism detection system. By submitting your manuscript to this journal you accept that your manuscript may be screened for plagiarism against previously published works.
Pre-submission English-language editing
Authors for whom English is a second language may choose to have their manuscript professionally edited before submission to improve the English. A list of independent suppliers of editing services can be found at hereAll services are paid for and arranged by the author, and use of one of these services does not guarantee acceptance or preference for publication.
Preparation and presentation of manuscripts
All manuscripts must be submitted online to  http://mc.manuscriptcentral.com/agingcell and must conform to the specifications given on the website. Only manuscripts in English will be published. Spelling should conform to that in The Concise Oxford Dictionary or Webster’s New Collegiate Dictionary.

The title page should include: (1) the full title of the paper- titles should be no more than three typeset lines (approximately 126 characters including spaces); (2) the full names of all the authors; (3) the name(s) and address(es) of the institution(s) at which the work was carried out (the present addresses of the authors, if different from the above, should appear in a footnote); (4) the name, address, telephone and fax numbers and e-mail address of the author to whom all correspondence and proofs should be sent; (5) the e-mail addresses of all the authors if possible; (6) a suggested running title of not more than 50 characters, including spaces; (7) six key words to aid indexing.
Primary Research PapersFor primary research papers a maximum character count of 50,000 characters (including spaces) is imposed to all sections (see below) with the exception of the Title Page, , Tables and Figures. Figure Legends are to be included in the character count. The character count will remain in effect for articles resubmitted in response to review. In addition, up to 2 pages of figures are allowed.
Papers should be divided into the following sections and appear in the order: (1) Title Page; (2) Checklist; (3) Summary, not to exceed 250 words; (4) Introduction; (5) Results; (6) Discussion; (7) Experimental Procedures; (8) Acknowledgments; (9) Author Contributions; (10) References; (11) Supporting Information listing, if appropriate; (12) Tables; (13) Figure legends; (14) Figures. The Results and Discussion sections may contain subheadings. Experimental Procedures should be sufficiently detailed to enable the experiments to be reproduced, and may in part appear as Supporting Information (see below).
All pages must be numbered consecutively from the title page, and include the Acknowledgments, References, Tables, and Figure Legends.
Short TakesThe Editors-in-Chief will consider short papers that report findings of exceptional relevance and interest. While most authors prefer to develop such findings into a larger story that provides significant mechanistic insights, in some cases the findings may be so novel or important to the field that their rapid dissemination takes precedence. Short Takes can have a maximum of 10,000 characters, defined as above for Primary Research Papers. In addition, Short Takes are limited to two Figures (or one Figure and one Table, or two Tables). The Introduction, Results and Discussion sections should be merged into one continuous text. Experimental Procedures are to be included as online Supporting Information.
ReviewsFor Review papers a maximum character count will remain in effect for articles resubmitted in response to review. The Summary is to be included in the character count and should be less than 250 words. The rest of the article is to be a continuous narrative. Subheadings may be used.  Some reviews may necessitate the citing of relevant original literature, and hence the References are not included in the character count, but in all cases the authors should be as concise with the References as possible. Reviews will not be subject to an Article Publication Charge.
CommentariesThe Editors-in-Chief will commission commentaries on seminal articles published in Aging Cell or elsewhere. The format is to follow that of Short Takes, above. Suggestions of appropriate papers are welcomed. Commentaries will not be subject to an Article Publication Charge.
Units and abbreviationsFor approved abbreviations and symbols please see (http://www.pnas.org/site/misc/table1.pdf). These standard abbreviations may be used in the title and abstract. Any abbreviations used in the title and abstract that are not on this list (nonstandard abbreviations) must be spelled out in full words followed by the abbreviation in parentheses. Standard abbreviations can also be used throughout the text of the article, notwithstanding how many times they are used. Nonstandard abbreviations can only be used if they occur more than three times within the text of the article. At the point of first use they must be spelled out in full words followed by the abbreviation in parentheses.
Scientific nomenclatureComplete scientific names should be given when organisms are first mentioned. The generic name may subsequently be abbreviated to the initial. It is important to differentiate between genes and proteins. All gene names and loci should be italic; proteins should be upright.
Checklist
A separate Checklist Page should be provided, immediately following the Title Page. It should contain the following information: (1) total character count; (2) word count of the Summary; (3) the number of papers cited in the References; (4) a listing of all Tables (Table 1, Table 2, etc.); (5) a listing of all Figures (Fig. 1, Fig. 2, etc.) including, (a) whether the Figure should be in colour, greyscale or black and white, (b) whether the Figure should appear in 1-column or 2-column format, (c) the size of the Figure at full scale (mm x mm), (d) the smallest font size used in the Figure at full scale.
Experimental Procedures
The Editorial Board endorses the ARRIVE Guidelines for reporting in vivo experiments.
Trade names should be capitalized. The manufacturer's name should be followed by an address including town, (state, if USA) and country.
Author ContributionsAuthors are encouraged to include a brief statement to specify the contributions of each co-author, to appear immediately before the References. The statement should not be more than several sentences long, describing the task of individual authors. Further information on authorship and contributorship may be found at http://www.icmje.org/#author.
ReferencesA maximum of 45 references will be allowed for Primary Research Papers, and 20 references for Short Takes. There is no limit on the number of references for Reviews, but authors should be as concise as possible. In the text references should be cited by author and date, e.g. Shah & Klessig (1999). Joint authors should be referred to by et al. if there are more than two, e.g. Sambrook et al. More than one paper from the same author(s) in the same year must be identified by the letters a, b, c, etc., placed after the year of publication. In the References section at the end of the paper, references should be listed alphabetically according to the first named author. The full titles of papers, chapters and books should be given, the abbreviated names of journals, with the first and last page numbers.
Examples
Whittemore SR, Nieto-Sampedro M, Needels DL, Cotman CW (1985) Neuronotrophic factors for mammalian brain neurons: injury induction in neonatal, adult and aged rat brain. Brain Res. 352, 169-178. Willot JF (1999) Neurogerontology: Aging and the Nervous System. New York: Springer Publishing Company, Inc. Cotman CW (1990) Synaptic plasticity, neurotrophic factors, and transplantation in the aged brain. In Handbook of the Biology of Aging (Schneider EL, ed). San Diego: Academic Press, pp. 617-644.
Work that has not been accepted for publication and personal communications should not appear in the reference list, but may be referred to in the text. It is the authors' responsibility to obtain permission from colleagues to include their work as a personal communication.
We recommend the use of a tool such as EndNote or Reference Manager for reference management and formatting.
EndNote reference styles can be searched for here:http://www.endnote.com/support/enstyles.aspReference Manager reference styles can be searched for here:http://www.refman.com/support/rmstyles.asp
Supporting InformationSupporting Information can be a useful way for an author to include important but ancillary information. Examples of Supporting Information include additional tables, data sets, figures, movie files, audio clips, 3D structures, and other related nonessential multimedia files. Supporting Information should be cited within the article text, and a descriptive legend should be included. It is published as supplied by the author, and a proof is not made available prior to publication; for these reasons, authors should provide any Supporting Information in the desired final format.
For further information on recommended file types and requirements for submission, please visit: http://authorservices.wiley.com/bauthor/suppinfo.asp
Two areas are highlighted where this practice is obligatory: submission of lifetime survival studies, and submission of microarray data. For survival studies, for each survival or mortality plot, authors should provide the raw data in the form of a Table to allow replication of the presented analysis and to facilitate independent analysis and cross-study comparisons. The table should be formatted with, as a minimum, the following columns: age-interval; number entering the age-interval (Nx); number dead within the age interval (Dx); number censored within the age interval (Cx). It is not required, but may be included at the author's choice, to present life table statistics as additional columns (e.g., period and cumulative survival, life expectancy, hazard, etc.). For each Figure, a separate Table should be provided and clearly associated with the Figure. The Table should be organized such that each cohort (the group that constitutes data for a single line in the Figure) is represented as an independent subsection. Thus, in Excel, separate worksheets should be used for each cohort. The labels of the worksheets should correspond to the labels used in the Figure Legend. In a tab-delimited text file, the subsections should be stacked and each subsection should be labeled with a subheading used in the Figure Legend.
For microarray data, sufficient information should be provided to allow replication of results as well as independent re-analysis of the data: (1) type of array used, method of RNA extraction, labeling, hybridization, washing and associated procedures; (2) full description of normalization procedures; (3) a detailed description of the statistical analyses and data mining methods applied; (4) an independent method (typically qPCR) should be used to validate the results for some of the genes identified as differentially expressed with, where possible, a rationale for the choice of the genes; (5) the raw, complete data set should be tabulated and provided in order to facilitate independent analysis and cross-study comparisons.
TablesPrimary Research Papers can contain a maximum of two Tables (in addition to the six Figures, below). If more Tables are needed, they should replace some of the Figures, or can be placed in the Supporting Information. Tables should be set out on separate pages and saved in Word format. They should have a brief descriptive title and be self-explanatory. Units should appear in parentheses in the column headings, not in the body of the table.
Figure LegendsFigure legends should be typed on separate sheets and must contain sufficient information to be understood without reference to the text. Legends should not contain methods. Each should begin with a short title for the figure. All symbols and abbreviations used in the figures should be explained. In the full-text online edition of the journal, figure legends may be truncated in abbreviated links to the full-screen version. Therefore, the first 100 characters of any legend should inform the reader of key aspects of the figure.
FiguresA Primary Research Paper may contain up to 6 figures and a Short Take up to 2 figures. Figures may have multiple panels. The journal prefers figures to appear at 1-column (80 mm) or 2-column (167 mm) width, and authors are encouraged to make as efficient use of this space as possible. The maximum height is 231 mm. Authors are encouraged to provide figures in the size that they are to appear in the journal. All fonts in the figures must be a minimum of 6 pt in size as in the journal. If authors provide figures that need to be scaled to conform to the one or two column format, they must indicate whether each figure is to appear as one or two columns, and if this results in any font being smaller than 6 pt that figure will be returned to the authors for reworking.
Vector graphics (e.g. line artwork) should be saved in EPS encapsulated postscript format (.eps) or PDF portable document format (.pdf). Photographic images should be saved in TIFF tagged image file format (.tif). Figures containing a combination of photographic images and text (e.g. annotated photographic images with text labels) should be saved as EPS or PDF. Any photographic images embedded within these should be at least 300 dpi. Initial submissions will be accepted in .jpg format in order to facilitate electronic transmission for reviewing. Detailed information on our digital illustration standards are available at http://authorservices.wiley.com/bauthor/illustration.aspWherever possible please also supply high quality hard copy figures at the time of manuscript acceptance.
Post-acceptance processing
ProofsThe corresponding author will receive an e-mail alert containing a link to a web site. A working e-mail address must therefore be provided for the corresponding author. The proof can be downloaded as a PDF file from this site. Acrobat Reader will be required in order to read this file. This software can be downloaded (free of charge) from the following web sitehttp://www.adobe.com/products/acrobat/readstep2.html.
This will enable the file to be opened, read on screen and printed out in order for any corrections to be added. Further instructions will be sent with the proof. Hard copy proofs will be posted if no e-mail address is available. Excessive changes made by the author in the proofs, excluding typesetting errors, will be charged separately. Major alterations to the text will be charged to the author and may delay publication.
Open Access AgreementIf your paper is accepted, the author identified as the formal corresponding author for the paper will receive an email prompting them to login into Author Services; where via the Wiley Author Licensing Service (WALS) they will be able to complete the license agreement on behalf of all authors on the paper.

The following license agreement is available:
Creative Commons Attribution License OAA
To preview the terms and conditions of this open access agreement, please visit http://creativecommons.org/licenses/by/3.0/.
Conflict of Interest
Aging Cell requires that all authors disclose any potential sources of conflict of interest. Any interest or relationship, financial or otherwise, that might be perceived as influencing an author’s objectivity is considered a potential source of conflict of interest. These must be disclosed when directly relevant or indirectly related to the work that the authors describe in their manuscript. Potential sources of conflict of interest include but are not limited to patent or stock ownership, membership of a company board of directors, membership of an advisory board or committee for a company, and consultancy for or receipt of speaker’s fees from a company. The existence of a conflict of interest does not preclude publication in this journal.
If the authors have no conflict of interest to declare, they must also state this at submission. It is the responsibility of the corresponding author to review this policy with all authors and to collectively list in the cover letter to the Editor, in the manuscript (under the Acknowledgment section), and in the online submission system ALL pertinent commercial and other relationships.
Article Publication Charges
Aging Cell is an open access journal, and you or your funder will be required to pay an article publication charge on acceptance. Please note that Commentaries and Review papers will not be subject to an Article Publication Charge. For more details on charges and available discounts, please see here.
Automatic Article Publication Charge waivers and discounts will be given to authors from countries on the Waivers and Discounts List. In addition Commentaries and Review papers will not be subject to an Article Publication Charge. Authors should submit a waiver or discount request during the submission of their article.
Author material archive policyPlease note that unless specifically requested, Wiley-Blackwell will dispose of all hardcopy or electronic material submitted four months after publication. Authors that wish the return of any material submitted, should inform the editorial office or production editor as soon as possible.
Early ViewAging Cell is covered by the Wiley-Blackwell Early View service. Early View articles are complete full-text articles published online in advance of their publication in an issue. Articles are therefore available as soon as they are ready, rather than having to wait for the next scheduled issue. Early View articles are complete and final. They have been fully reviewed, revised and edited for publication, and the authors' final corrections have been incorporated.
Because they are in final form, no changes can be made after online publication. The nature of Early View articles means that they do not yet have volume, issue or page numbers, so Early View articles cannot be cited in the traditional way. They are therefore given a Digital Object Identifier (DOI), which allows the article to be cited and tracked before it is allocated to an issue. After issue publication, the DOI remains valid and can continue to be used to cite and access the article. More information about DOIs can be found at http://www.doi.org/faq.html.
OffprintsFree access to the final PDF offprint or your article will be available via author services only. Please therefore sign up for author services if you would like to access your article PDF offprint and enjoy the many other benefits the service offers.
Cover photographPhotographs of high quality suitable for the Aging Cell website cover, or other promotional purposes are welcomed. They should be sent to the Editors and be accompanied by a brief descriptive summary. It is preferred, but not essential, that these should be related to submitted papers.
Online production tracking is now available through Author ServicesAuthor Services enables authors to track their article - once it has been accepted - through the production process to publication. Authors can check the status of their articles online and choose to receive automated e-mails at key stages of production. Authors will receive an e-mail with a unique link that will enable them to register and have their article automatically added to the system. Please ensure that a complete e-mail address is provided when submitting the manuscript. Visit http://authorservices.wiley.com/bauthor/ for more details on online production tracking and for a wealth of resources including FAQs and tips on article preparation, submission and more.
PubMed Central (PMC)
PubMed Central (PMC) is created by the U.S. National Institutes of Health (NIH) and is a digital archive of biomedical and life sciences journal literature. It is a full text database, which gives readers free access to the full text version of articles. Wiley Open Access journals will deposit all articles into PMC upon publication of an online issue, on a monthly basis. The final published versions of the articles are sent to PMC.

Thursday, February 16, 2017

genetics and protein networks on RLS of yeast

Canalization: a measure of population's ability to produce the same phenotype regardless of variability of its environment or genotype.
 How well is the yeast cell to produce the same phenotypes even though the existence of variability in the conditions or genotype?

Fitness and genetic robustness: There was a good overall correlation between fitness and robustness. 

Friday, February 10, 2017

QinLab meeting

public project on GitHub
purchase domain name
compmodelmatch.org website

Friday, February 3, 2017

Qin lab meeting

1)Tapia Conference registration opens on April 2017: http://tapiaconference.org/
2)UTC research day registration,
3)provost award application


Recurrent neural network Image Analysis project
4)xu_r  2004 neural network paper needs some model improvement
    adjacency matrix: https://en.wikipedia.org/wiki/Adjacency_matrix
    Theano , Torch, rnn package
  RNN: gene interaction or time-lapsed image analysis

Wednesday, February 1, 2017

gene expression

GE is the process of a specific gene producing a specific information to synthesize a functional gene product. During  gene expression process may be modulated by the transcriptionRNA splicingtranslation, and post-translational modification of a protein.  

Gene Product: protein and RNA
https://en.wikipedia.org/wiki/Gene_product

Regulation of GE:  
The basis of cellular differentiation and morphogenesis is the gene regulation that gives the cell control over structure and function.
Mechanisms that are used by cells to increase or decrease the production of specific gene products, and is informally termed gene regulation. It is very critical for an organism for normal development to regulate gene expression levels.

phenotype vs genotype:
The genotype gives rise to the phenotype, i.e. observable or physical trait at the level of gene regulation level.