Saturday, February 17, 2018

cell size and aging

In yeast, cell size is an indicator for cell's remaining replicative lifespan, based on Jo 2015. So, the limit of cell size could be aging itself.

Friday, February 16, 2018

Monday, February 5, 2018

bluejeans video conferences

gatech uses bluejeans.com for video conference

UAB, aging biology update


Aging Biology Update is brought to you by the UAB Nathan Shock Center and was compiled by Jessica M. Hoffman, Steven N. Austad, and Heather K. Patterson.

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Friday, February 2, 2018

latex, multiple panel figure


More at:
https://tex.stackexchange.com/questions/271518/multiple-panel-figure-with-figures-side-by-side/271522

multiple panel figure in latex. The arrangement is partly controlled by "%", unbelievable.

\documentclass{article}
\usepackage{graphicx}
\usepackage{subcaption}

\begin{document}

\begin{figure}
\centering

\begin{subfigure}[t] {0.4\textwidth}
\centering
\includegraphics[width=\linewidth]{FiguresTables/pdf/BY4742.pdf}
  \caption{}
  \label{Figure:fig_a}
\end{subfigure}
%
\begin{subfigure}[t] {0.4\textwidth}
\centering
     \includegraphics[width=\linewidth]{FiguresTables/pdf/sir2.pdf}
  \caption{}
  \label{Figure:fig_b}
\end{subfigure}

\medskip

\begin{subfigure}[t] {0.4\textwidth}
\centering
     \includegraphics[width=\linewidth]{FiguresTables/pdf/fob1.pdf}
  \caption{}
  \label{Figure:fig_c}
\end{subfigure}
%
\begin{subfigure}[t] {0.4\textwidth}
\centering
     \includegraphics[width=\linewidth]{FiguresTables/pdf/hxk2.pdf}
  \caption{}
  \label{Figure:fig_d}
\end{subfigure}


\begin{minipage}[t]{0.4\textwidth}
\caption{Try a multi-panel figure}
\end{minipage}

\end{figure}

\end{document}

cellmap, gin, postive and negative interactions


Cellmap contain positive and negative interactions for the same gene-pairs, an apparent quality problem. It seems false disovery rate may be used here to improve the annotations.

Thursday, February 1, 2018

Yeast essential genes, quality check



Their RLSs ranges from ~6 to >40. Other genes such as SOD1, although its mutation leads to an RLS of ~3, it is not considered as an essential gene (not in all essential sets I mentioned).

Here's another example: shown below are the entries of several genes in the SGA_ExE, CellMap table, followed by the measured RLS for the mutated strain:
YDR364C (736, 16.4), YGR092W (5237, 9.8), YHR191C (2127, 8.0), YLR268W (2769, 23.0).
These genes also appear in the SGA_NxN table with 3k-7k entries.

Overall, two steps are needed to clean up the data:

  1. The RLS set itself also has some problem: For example, swh1 and osh1 are two names of the same gene YAR042W, and these two tests have mean RLSs of 22.4 and 26.4, respectively. I found 9 such cases. Apparently we can only use 1 (may be average of the two tests) for them.
  2.  For the essential genes, I think, we may start with the DEG set that based on the yeast deletion collection, and set some criteria: a). did not appear in the RLS set; b). did not appear in the NxN CellMap table; and c). did not labeled nonessential in the growth-fit set. These three criteria give 70, 65 and 73 overlaps, respectively, and overall there are 91 genes should be removed from the DEG set. Of these genes, 70 have RLS data, but 21 do not.

Monday, January 29, 2018

possible ms02 bug and how to fix it.

update on 20180202: it turns out the input pairs of network contain redundant pairs. So, input data need to be checked for consistency by a switch, such as "-input-check 1"

It is possible that recursive call return pairs that already existed in previous iterations, in recursive implementation.

This may explain why large network permutation give slightly different random networks.

One way to fix this is to do book-keeping on the entire networks (instead of a small chunk using recursive definitions). This may be implemented in a separate functional call, breaking self-pairing and reassignment partners.




machine learning in Python



http://scikit-learn.org/stable/

Thursday, January 25, 2018

NSF fastlane requirement update



You are receiving this email because you have been identified as having an in-process proposal or in-process Proposal File Update (PFU) in FastLane.
Effective January 29, 2018, NSF will implement changes in FastLane and Research.gov to support the following policy updates in the Proposal & Award Policies & Procedures Guide (PAPPG) (NSF 18-1) and to run updated Budget Justification page limit automated compliance checks in FastLane:
Standard Collaborators and Other Affiliations Template Implementation:
  • The revised PAPPG (NSF 18-1) incorporates the standard Collaborators and Other Affiliations (COA) template that has been in pilot phase in FastLane since April 2017.
  • FastLane system instructions will be updated in accordance with the new policy.
  • Frequently Asked Questions (FAQs) on the COA template are available at https://nsf.gov/bfa/dias/policy/coa.jsp.

Budget Justification Page Limitation Increase:
  • The Budget Justification page limitation will increase from three pages to five pages.
  • To align with the new policy, FastLane will run an automated compliance check for the Budget Justification page limitation across several proposal types and will generate an error or warning when the submission validation compliance check is not met.
  • Compliance checks are run during “Check Proposal,” “Forward to SPO,” and “Submit Proposal.” The complete list of FastLane automated compliance checks effective January 29, 2018, is available at https://www.nsf.gov/bfa/dias/policy/autocheck/compliancechecks_jan18.pdf.

New “Substitute Negotiator” Associated Document for Change of Principal Investigator (PI) Requests:
  • A new “Substitute Negotiator” Associated Document will be available in FastLane’s Notifications and Requests module when a “Change of PI” request is made (e.g., to be utilized in cases where a former employee or Intergovernmental Personnel Act (IPA) is being reappointed as a PI or Co-PI to an award they were previously involved with).
New “Other Request” Type:
  • A new “Other Request” type will be added to Research.gov’s Notifications and Requests module. This request will be reviewed and approved by the NSF Program Officer.

New Award Abstract Text:
  • In connection with NSF’s transparency and accountability efforts for award abstracts, the Foundation will add the following final paragraph to all award abstracts for awards with start dates of March 1 or later: “This award reflects NSF’s statutory mission and has been deemed worthy of support through evaluation using the Foundation’s intellectual merit and broader impacts review criteria.”

Note about Proposal File Updates (PFU):
The automated compliance checks also apply when a PFU is performed on a proposal. The compliance checks will be run on all sections of the proposal, regardless of which section was updated during the PFU. Proposers should be aware that if a proposal was previously submitted successfully, a PFU performed on the proposal will be prevented from submission if the proposal does not comply with the compliance checks in effect at the time.

We encourage you to share this information with your colleagues. To learn about all the changes to the PAPPG (NSF 18-1), be sure to view the latest webinar.

For IT system-related questions, please contact FastLane User Support at 1-800-673-6188 or fastlane@nsf.gov. Policy-related questions should be directed to policy@nsf.gov. 

Regards,
The FastLane Team at the National Science Foundation

If you would like to stay up-to-date on upcoming events or future enhancements to Research.gov and FastLane, subscribe to our System Updates NSF listserv. This listserv is available to both the research community and to NSF staff. To subscribe, simply send an email to system_updates-subscribe-request@listserv.nsf.gov and you will be automatically enrolled.


Tuesday, January 23, 2018

UTC Activity Insight

UTC Activity Insight

https://www.digitalmeasures.com/login/utc/faculty/app/activities