Blaine Mooers

Blaine Mooers

Earned PhD in Biochemistry and Biophysics with Shing Ho at Oregon State Univeristy and did post-doc with Brian Matthews at the University of Oregon.

Posts by Tags

Acquah

Poster presented at the 10th Annual Oklahoma Structural Biology Symposium

less than 1 minute read

Published:

Mooers’s presented Francis’s dissertation work on a poster at the 10th Annual Oklahoma Structural Biology Symposium at the University of Oklahoma; Francis had already moved to Boston to start a job in biotech. The symposium was held at the National Storm Prediction Center. Sadly, this symposium was the final symposium in this series. It series ended with a big bang via a lineup of excellent scientists as invited speakers. The symposium series was funded by the phase I and II grants from the NIH for the Oklahoma COBRE in Structural Biology, which is led by Dr. Ann West at OU-Norman. It was attended by well over 100 people from Oklahoma and around the country.

Atom

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

Blaine Mooers

CD spectroscopy

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

COBRE

Poster presented at the 10th Annual Oklahoma Structural Biology Symposium

less than 1 minute read

Published:

Mooers’s presented Francis’s dissertation work on a poster at the 10th Annual Oklahoma Structural Biology Symposium at the University of Oklahoma; Francis had already moved to Boston to start a job in biotech. The symposium was held at the National Storm Prediction Center. Sadly, this symposium was the final symposium in this series. It series ended with a big bang via a lineup of excellent scientists as invited speakers. The symposium series was funded by the phase I and II grants from the NIH for the Oklahoma COBRE in Structural Biology, which is led by Dr. Ann West at OU-Norman. It was attended by well over 100 people from Oklahoma and around the country.

ClojConj

Protein structure comparison in Clojure

less than 1 minute read

Published:

I gave a talk that is on YouTube about comparing protein structures in Clojure at ClojConj 2023 in Durham, NC on April 2023. I share this project with Daniel Slutsky, an organizer of the SciCloj community and leader of the JointProb group. He is a vital co-author. He provided a lot of help with the talk.

Clojure

Protein structure comparison in Clojure

less than 1 minute read

Published:

I gave a talk that is on YouTube about comparing protein structures in Clojure at ClojConj 2023 in Durham, NC on April 2023. I share this project with Daniel Slutsky, an organizer of the SciCloj community and leader of the JointProb group. He is a vital co-author. He provided a lot of help with the talk.

DOE

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

Data Science Workshop

Editing Jupyter Notebook Cells Live with Emacs

Mooers gives talk at eamcsconf 2022 about editing live Jupyter Notebook Cells and Overleaf with Emacs

less than 1 minute read

Published:

On December 2, 2022, I gave a talk at emacsconf 2022 about editing live Juptyer Notebook cells with Emacs via the atomic-chrome package for Emacs and the browser extension known as GhostText. I presented several little-known applications of these two packages that others have developed. I also demonstrated how GhostText can be used with Overleaf to enable using Emacs to edit Overleaf Text Areas. This new power should be of interest to the million users of Overleaf. Juan Zhang commented on the talk’s YouTube page: Thanks for the very helpful talk! GhostText is like a Godsend; overleaf is finally usable. The Youtube video garnered almost 900 views in the first three weeks. Please note that in December 2022 (after my talk), Overleaf changed the file format for the source text area. Select the `Source (legacy)’ tab to get the behavior demonstrated in the above video. Many thank yous go to the organizers of this meeting!!! Their team hosted another successful emacsconf!!! They did an enormous amount of work behind the scenes.

Editing Overleaf text areas with Emacs

Mooers gives talk at eamcsconf 2022 about editing live Jupyter Notebook Cells and Overleaf with Emacs

less than 1 minute read

Published:

On December 2, 2022, I gave a talk at emacsconf 2022 about editing live Juptyer Notebook cells with Emacs via the atomic-chrome package for Emacs and the browser extension known as GhostText. I presented several little-known applications of these two packages that others have developed. I also demonstrated how GhostText can be used with Overleaf to enable using Emacs to edit Overleaf Text Areas. This new power should be of interest to the million users of Overleaf. Juan Zhang commented on the talk’s YouTube page: Thanks for the very helpful talk! GhostText is like a Godsend; overleaf is finally usable. The Youtube video garnered almost 900 views in the first three weeks. Please note that in December 2022 (after my talk), Overleaf changed the file format for the source text area. Select the `Source (legacy)’ tab to get the behavior demonstrated in the above video. Many thank yous go to the organizers of this meeting!!! Their team hosted another successful emacsconf!!! They did an enormous amount of work behind the scenes.

Emacs

Emacs with tree-sitter support

less than 1 minute read

Published:

Tree-sitter is a C library that supports editing code with a concrete syntax tree. This syntax tree enables more powerful editing commands that save time and reduce tedium. Emacs and other leading text editors are still in the process of harnessing tree-sitter.

Emacs must be compiled with the tree-sitter C library already installed on your computer. I provide a protocol for doing so on a fresh installation of Ubuntu 22.04 LTS. I also succeeded with macOS 13.2 (Ventura) after I figured out that I needed to specify the path to the giflib library. Note that this library is different from the tree-sitter.el package that will be built into Emacs version 29.

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

Ferrel Lytle Award

Mooers wins Ferrel Lytle Award

less than 1 minute read

Published:

On September 29th at the 2022 SSRL/LCLS Users Meeting, Mooers was awarded the Ferrel Lytle Award for his service on the SSRL User executive committee and his research using SSRL.

Francis Acquah

Paper published in iScience

less than 1 minute read

Published:

Our first collaborative paper with the Dr. Alla V Tsytsykova and colleagues in the Lab of the Ian Dunn in the Department of Neurosurgery, OUHSC, was published on-line in the journal iScience: Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression . Francis made and purified four recombinant versions of KLF4. This work was done towards understanding how the K409Q mutant triggers the development of brain tumors. This work was funded by a Team Science grant from the Presbyterian Health Foundation.

Paper published in Royal Society of Chemistry Advances

less than 1 minute read

Published:

Our second collaborative paper with the Dr. Razi Hussaini Lab of the Department of Chemistry, U of Tulsa, was published on-line in the journal Royal Society of Chemistry Advances. Francis did a series of docking experiments and molecular dynamics simulations with the structure of the nicotinic acetyl-choline receptor α6-nAchR embedded in a bilayer for this study. This work was done towards the goal of developing better smoking cessation drugs and was funded by a three-year Health Research Program grant from the Oklahoma Center for the Advancement of Science and Technology.

Francis Acquah defends dissertation

less than 1 minute read

Published:

Francis Acquah defends his dissertation successfully! The title is “Targeting RNA s ubstrates in the discovery of inhibitors of trypanosome mitochontrial RNA editing”.

GhostText

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

MST

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

OSCER at OU

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

Oklahoma Data Science Workshop

OpenAI

Python

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

RNA crystallization

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

RNA editing

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

SSRL

2023 SSRL/LCLS Users Meeting

less than 1 minute read

Published:

Mooers co-chaired the SSR/LCLS Users Meeting at the SLAC National Accelerator Center in Menlo Park, CA. This was the first in person meeting in four years due to the pandemic. Abut 600 people attended this six day meeting. We had 33 half or full day workshops. Mooers co-chaired for the fourth year with Dr. Tzanko Doukov the session ``Computational Methods in Structural Methods.’’. We had eight amzing speakers talk about cutting edge methods. Mooers also co-chaired a workshop on biological SAXS with Dr. Thomas Weiss.

MooersLab landing page initiated.

less than 1 minute read

Published:

I discovered that a repo made with the name of a GitHub site can have a README.md file that shows up on the landing page. This file can be used to provide an index or table of contexts to the repos by clustering them by category. This format can draw the visitors attention to relevant repos and is much better than the default tag search approach where the visitor has to know the relevent search terms in advance or has to scroll through all of the repos.

Workshop: Computational Methods in the Structural Sciences

less than 1 minute read

Published:

On the afternoon of Monday, September 26, 2022, Drs Tzanko Doukov and Blaine Mooers co-chaired a four-hour workshop Computational Methods in the Structural Sciences at the annual SSRL/LCLS Users meeting. It had eight speakers from three continents. The topics were quite diverse: micro-ED, cryo-EM, SAXS, radiation damage analysis, solvent channel analysis, and direct phasing. All of the talks were reviting. However, the last speaker really hit a home-run with some very exciting results about extending direct phasing methods. This talk was mentioned several times in other workshops and plenary sessions on the following days.

SSRL/LCLS Users Meeting

Mooers wins Ferrel Lytle Award

less than 1 minute read

Published:

On September 29th at the 2022 SSRL/LCLS Users Meeting, Mooers was awarded the Ferrel Lytle Award for his service on the SSRL User executive committee and his research using SSRL.

Sublime Text

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

Targeting RNA structure

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

US-RSE

Ubuntu

Emacs with tree-sitter support

less than 1 minute read

Published:

Tree-sitter is a C library that supports editing code with a concrete syntax tree. This syntax tree enables more powerful editing commands that save time and reduce tedium. Emacs and other leading text editors are still in the process of harnessing tree-sitter.

Emacs must be compiled with the tree-sitter C library already installed on your computer. I provide a protocol for doing so on a fresh installation of Ubuntu 22.04 LTS. I also succeeded with macOS 13.2 (Ventura) after I figured out that I needed to specify the path to the giflib library. Note that this library is different from the tree-sitter.el package that will be built into Emacs version 29.

User Executive Committee

2023 SSRL/LCLS Users Meeting

less than 1 minute read

Published:

Mooers co-chaired the SSR/LCLS Users Meeting at the SLAC National Accelerator Center in Menlo Park, CA. This was the first in person meeting in four years due to the pandemic. Abut 600 people attended this six day meeting. We had 33 half or full day workshops. Mooers co-chaired for the fourth year with Dr. Tzanko Doukov the session ``Computational Methods in Structural Methods.’’. We had eight amzing speakers talk about cutting edge methods. Mooers also co-chaired a workshop on biological SAXS with Dr. Thomas Weiss.

Users Annual Meeting

MooersLab landing page initiated.

less than 1 minute read

Published:

I discovered that a repo made with the name of a GitHub site can have a README.md file that shows up on the landing page. This file can be used to provide an index or table of contexts to the repos by clustering them by category. This format can draw the visitors attention to relevant repos and is much better than the default tag search approach where the visitor has to know the relevent search terms in advance or has to scroll through all of the repos.

Workshop: Computational Methods in the Structural Sciences

less than 1 minute read

Published:

On the afternoon of Monday, September 26, 2022, Drs Tzanko Doukov and Blaine Mooers co-chaired a four-hour workshop Computational Methods in the Structural Sciences at the annual SSRL/LCLS Users meeting. It had eight speakers from three continents. The topics were quite diverse: micro-ED, cryo-EM, SAXS, radiation damage analysis, solvent channel analysis, and direct phasing. All of the talks were reviting. However, the last speaker really hit a home-run with some very exciting results about extending direct phasing methods. This talk was mentioned several times in other workshops and plenary sessions on the following days.

Users Meeting

2023 SSRL/LCLS Users Meeting

less than 1 minute read

Published:

Mooers co-chaired the SSR/LCLS Users Meeting at the SLAC National Accelerator Center in Menlo Park, CA. This was the first in person meeting in four years due to the pandemic. Abut 600 people attended this six day meeting. We had 33 half or full day workshops. Mooers co-chaired for the fourth year with Dr. Tzanko Doukov the session ``Computational Methods in Structural Methods.’’. We had eight amzing speakers talk about cutting edge methods. Mooers also co-chaired a workshop on biological SAXS with Dr. Thomas Weiss.

VScode

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

Vim

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

agile code editing

Emacs with tree-sitter support

less than 1 minute read

Published:

Tree-sitter is a C library that supports editing code with a concrete syntax tree. This syntax tree enables more powerful editing commands that save time and reduce tedium. Emacs and other leading text editors are still in the process of harnessing tree-sitter.

Emacs must be compiled with the tree-sitter C library already installed on your computer. I provide a protocol for doing so on a fresh installation of Ubuntu 22.04 LTS. I also succeeded with macOS 13.2 (Ventura) after I figured out that I needed to specify the path to the giflib library. Note that this library is different from the tree-sitter.el package that will be built into Emacs version 29.

automatic speach recognition

brain cancer

Paper published in iScience

less than 1 minute read

Published:

Our first collaborative paper with the Dr. Alla V Tsytsykova and colleagues in the Lab of the Ian Dunn in the Department of Neurosurgery, OUHSC, was published on-line in the journal iScience: Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression . Francis made and purified four recombinant versions of KLF4. This work was done towards understanding how the K409Q mutant triggers the development of brain tumors. This work was funded by a Team Science grant from the Presbyterian Health Foundation.

career planning and management

Track daily writing progress by project in 2024 and 2025

less than 1 minute read

Published:

Most books on writing recommend tracking writing progress, but none address well how to juggle multiple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, manuscript reviews, lectures, and books in parallel. My approach is to track my writing progress on a per-project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progress. The entry of the progress per project requires only a few seconds. I designed the graphs to show the cumulative progress across all projects. Each month has its bar graph. You select the appropriate column and generate the sum to get the cumulative progress for a specific project. I developed this version for 2024 and 2025. I have shared this as an Excel workbook and a Libre Office version on a GitHub repository called writing-progress-2024-25. You can import either into a Google Sheet for faster access.

Track daily writing progress by project in 2023 in an Excel workbook

1 minute read

Published:

A lot of books on writing tout the value of tracking writing progress, but none of them address to my satisfaction how to cope with the problem of juggling mulitple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, and books in parellel. My approach is to track my writing progress on a per project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progess. The graphs are set up to show the cumulative progress across all projects. Each months has its own graph. To get the cummulative progress for a project, you select the appropriate column and the sum will be reported. The entry of the progress per project requires only a few seconds. I have shared this Excel workbook and a Libre Office version on a GitHub repository called writingProgess2023. I have included a webpage where you can paste text into a text area to get the word count. I also have updated the extensive README.md file. I actually import the workbook into Google Sheets and then add the link to my browser toolbar. This gives me instant access to the workbook without the startup time of Excel. This convenience further reduces the motivational barier to updating the project worksheet.

clusters

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

code snippets

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

computational methods

MooersLab landing page initiated.

less than 1 minute read

Published:

I discovered that a repo made with the name of a GitHub site can have a README.md file that shows up on the landing page. This file can be used to provide an index or table of contexts to the repos by clustering them by category. This format can draw the visitors attention to relevant repos and is much better than the default tag search approach where the visitor has to know the relevent search terms in advance or has to scroll through all of the repos.

Workshop: Computational Methods in the Structural Sciences

less than 1 minute read

Published:

On the afternoon of Monday, September 26, 2022, Drs Tzanko Doukov and Blaine Mooers co-chaired a four-hour workshop Computational Methods in the Structural Sciences at the annual SSRL/LCLS Users meeting. It had eight speakers from three continents. The topics were quite diverse: micro-ED, cryo-EM, SAXS, radiation damage analysis, solvent channel analysis, and direct phasing. All of the talks were reviting. However, the last speaker really hit a home-run with some very exciting results about extending direct phasing methods. This talk was mentioned several times in other workshops and plenary sessions on the following days.

crystal size optimization

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

crystallograhic computing

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

definitive screening designs

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

design of experiments

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

distress management

Track daily writing progress by project in 2024 and 2025

less than 1 minute read

Published:

Most books on writing recommend tracking writing progress, but none address well how to juggle multiple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, manuscript reviews, lectures, and books in parallel. My approach is to track my writing progress on a per-project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progress. The entry of the progress per project requires only a few seconds. I designed the graphs to show the cumulative progress across all projects. Each month has its bar graph. You select the appropriate column and generate the sum to get the cumulative progress for a specific project. I developed this version for 2024 and 2025. I have shared this as an Excel workbook and a Libre Office version on a GitHub repository called writing-progress-2024-25. You can import either into a Google Sheet for faster access.

Track daily writing progress by project in 2023 in an Excel workbook

1 minute read

Published:

A lot of books on writing tout the value of tracking writing progress, but none of them address to my satisfaction how to cope with the problem of juggling mulitple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, and books in parellel. My approach is to track my writing progress on a per project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progess. The graphs are set up to show the cumulative progress across all projects. Each months has its own graph. To get the cummulative progress for a project, you select the appropriate column and the sum will be reported. The entry of the progress per project requires only a few seconds. I have shared this Excel workbook and a Libre Office version on a GitHub repository called writingProgess2023. I have included a webpage where you can paste text into a text area to get the word count. I also have updated the extensive README.md file. I actually import the workbook into Google Sheets and then add the link to my browser toolbar. This gives me instant access to the workbook without the startup time of Excel. This convenience further reduces the motivational barier to updating the project worksheet.

drug design

Paper published in Royal Society of Chemistry Advances

less than 1 minute read

Published:

Our second collaborative paper with the Dr. Razi Hussaini Lab of the Department of Chemistry, U of Tulsa, was published on-line in the journal Royal Society of Chemistry Advances. Francis did a series of docking experiments and molecular dynamics simulations with the structure of the nicotinic acetyl-choline receptor α6-nAchR embedded in a bilayer for this study. This work was done towards the goal of developing better smoking cessation drugs and was funded by a three-year Health Research Program grant from the Oklahoma Center for the Advancement of Science and Technology.

Francis Acquah defends dissertation

less than 1 minute read

Published:

Francis Acquah defends his dissertation successfully! The title is “Targeting RNA s ubstrates in the discovery of inhibitors of trypanosome mitochontrial RNA editing”.

emacsconf 2022

Mooers gives talk at eamcsconf 2022 about editing live Jupyter Notebook Cells and Overleaf with Emacs

less than 1 minute read

Published:

On December 2, 2022, I gave a talk at emacsconf 2022 about editing live Juptyer Notebook cells with Emacs via the atomic-chrome package for Emacs and the browser extension known as GhostText. I presented several little-known applications of these two packages that others have developed. I also demonstrated how GhostText can be used with Overleaf to enable using Emacs to edit Overleaf Text Areas. This new power should be of interest to the million users of Overleaf. Juan Zhang commented on the talk’s YouTube page: Thanks for the very helpful talk! GhostText is like a Godsend; overleaf is finally usable. The Youtube video garnered almost 900 views in the first three weeks. Please note that in December 2022 (after my talk), Overleaf changed the file format for the source text area. Select the `Source (legacy)’ tab to get the behavior demonstrated in the above video. Many thank yous go to the organizers of this meeting!!! Their team hosted another successful emacsconf!!! They did an enormous amount of work behind the scenes.

emacsconf 2023

experimental design

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

machine learning

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

molecular dynamics simualtion

Paper published in Royal Society of Chemistry Advances

less than 1 minute read

Published:

Our second collaborative paper with the Dr. Razi Hussaini Lab of the Department of Chemistry, U of Tulsa, was published on-line in the journal Royal Society of Chemistry Advances. Francis did a series of docking experiments and molecular dynamics simulations with the structure of the nicotinic acetyl-choline receptor α6-nAchR embedded in a bilayer for this study. This work was done towards the goal of developing better smoking cessation drugs and was funded by a three-year Health Research Program grant from the Oklahoma Center for the Advancement of Science and Technology.

Francis Acquah defends dissertation

less than 1 minute read

Published:

Francis Acquah defends his dissertation successfully! The title is “Targeting RNA s ubstrates in the discovery of inhibitors of trypanosome mitochontrial RNA editing”.

molecular dynamics simultion

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

multiple file transfer

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

multiple writing progect management

Track daily writing progress by project in 2024 and 2025

less than 1 minute read

Published:

Most books on writing recommend tracking writing progress, but none address well how to juggle multiple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, manuscript reviews, lectures, and books in parallel. My approach is to track my writing progress on a per-project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progress. The entry of the progress per project requires only a few seconds. I designed the graphs to show the cumulative progress across all projects. Each month has its bar graph. You select the appropriate column and generate the sum to get the cumulative progress for a specific project. I developed this version for 2024 and 2025. I have shared this as an Excel workbook and a Libre Office version on a GitHub repository called writing-progress-2024-25. You can import either into a Google Sheet for faster access.

Track daily writing progress by project in 2023 in an Excel workbook

1 minute read

Published:

A lot of books on writing tout the value of tracking writing progress, but none of them address to my satisfaction how to cope with the problem of juggling mulitple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, and books in parellel. My approach is to track my writing progress on a per project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progess. The graphs are set up to show the cumulative progress across all projects. Each months has its own graph. To get the cummulative progress for a project, you select the appropriate column and the sum will be reported. The entry of the progress per project requires only a few seconds. I have shared this Excel workbook and a Libre Office version on a GitHub repository called writingProgess2023. I have included a webpage where you can paste text into a text area to get the word count. I also have updated the extensive README.md file. I actually import the workbook into Google Sheets and then add the link to my browser toolbar. This gives me instant access to the workbook without the startup time of Excel. This convenience further reduces the motivational barier to updating the project worksheet.

optimization experiments

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

personal productivity

probablistic programming

Protein structure comparison in Clojure

less than 1 minute read

Published:

I gave a talk that is on YouTube about comparing protein structures in Clojure at ClojConj 2023 in Durham, NC on April 2023. I share this project with Daniel Slutsky, an organizer of the SciCloj community and leader of the JointProb group. He is a vital co-author. He provided a lot of help with the talk.

project management

Track daily writing progress by project in 2024 and 2025

less than 1 minute read

Published:

Most books on writing recommend tracking writing progress, but none address well how to juggle multiple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, manuscript reviews, lectures, and books in parallel. My approach is to track my writing progress on a per-project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progress. The entry of the progress per project requires only a few seconds. I designed the graphs to show the cumulative progress across all projects. Each month has its bar graph. You select the appropriate column and generate the sum to get the cumulative progress for a specific project. I developed this version for 2024 and 2025. I have shared this as an Excel workbook and a Libre Office version on a GitHub repository called writing-progress-2024-25. You can import either into a Google Sheet for faster access.

Track daily writing progress by project in 2023 in an Excel workbook

1 minute read

Published:

A lot of books on writing tout the value of tracking writing progress, but none of them address to my satisfaction how to cope with the problem of juggling mulitple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, and books in parellel. My approach is to track my writing progress on a per project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progess. The graphs are set up to show the cumulative progress across all projects. Each months has its own graph. To get the cummulative progress for a project, you select the appropriate column and the sum will be reported. The entry of the progress per project requires only a few seconds. I have shared this Excel workbook and a Libre Office version on a GitHub repository called writingProgess2023. I have included a webpage where you can paste text into a text area to get the word count. I also have updated the extensive README.md file. I actually import the workbook into Google Sheets and then add the link to my browser toolbar. This gives me instant access to the workbook without the startup time of Excel. This convenience further reduces the motivational barier to updating the project worksheet.

protein purification

Paper published in iScience

less than 1 minute read

Published:

Our first collaborative paper with the Dr. Alla V Tsytsykova and colleagues in the Lab of the Ian Dunn in the Department of Neurosurgery, OUHSC, was published on-line in the journal iScience: Mutated KLF4(K409Q) in meningioma binds STRs and activates FGF3 gene expression . Francis made and purified four recombinant versions of KLF4. This work was done towards understanding how the K409Q mutant triggers the development of brain tumors. This work was funded by a Team Science grant from the Presbyterian Health Foundation.

protein structure comparison

Protein structure comparison in Clojure

less than 1 minute read

Published:

I gave a talk that is on YouTube about comparing protein structures in Clojure at ClojConj 2023 in Durham, NC on April 2023. I share this project with Daniel Slutsky, an organizer of the SciCloj community and leader of the JointProb group. He is a vital co-author. He provided a lot of help with the talk.

remote computers

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

response surface methods

Definitive screening designs for growing bigger crystals

less than 1 minute read

Published:

In the session on Crystal Growth at the 2023 meeting of the American Crystallographic Association in Baltimore, I presented Syed Aslam’s results of applying a Definitive Screening Design to the problem of growing larger RNA crystals. This work builds on the work by Barat Venkataramany and many other lab members, many of who were trained by Francis Acquah. We are applying these designs with guidance from Profess Charlie Carter Jr. This talk generated a lot of excitement and some useful suggestions from the audience. The slides and sample spreadsheet are located here. The libary will be expanded shortly.

scp

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

speech-to-text

sshpass

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

supercomputing

Script for easier multiple file transfer posted on GitHub

less than 1 minute read

Published:

One annoying and time-consuming task in scientific computing and data science is the transfer of multiple large tar archive files of raw data files from remote computers to local ones. We do this task frequently in our structural biology work. I assembled a bash script that eases this chore. You can use the script to pass your password. This script negates the need to enter your password before each tar file is transferred. The script notifies you audibly when it finishes.

synchtrotron radiation

2023 SSRL/LCLS Users Meeting

less than 1 minute read

Published:

Mooers co-chaired the SSR/LCLS Users Meeting at the SLAC National Accelerator Center in Menlo Park, CA. This was the first in person meeting in four years due to the pandemic. Abut 600 people attended this six day meeting. We had 33 half or full day workshops. Mooers co-chaired for the fourth year with Dr. Tzanko Doukov the session ``Computational Methods in Structural Methods.’’. We had eight amzing speakers talk about cutting edge methods. Mooers also co-chaired a workshop on biological SAXS with Dr. Thomas Weiss.

text editors

CCTBX snippets for text editors

less than 1 minute read

Published:

The Computational Crystallography Toolbox (cctbx) is a library of functions that support numerical computing in crystallography. The library is written in C++ for speed. It is also wrapped in Python to ease its use. The Phenix software suite depends on cctbx but not vice vera. The Olex2 small molecule refinement package also depends on cctbx. In spite of several excellent tutorials on the cctbx website, many scientists find cctbx hard to penetrate. I developed a library of snippets to help ease the use of cctbx. This library was initially made available for use in Jupyter and Colab, but it is now available at MooersLab on GitHub for the leading text editors: VScode, Vim, NeoVim, Emacs, Sublime Text, and Atom. These editors can also use GhostText to edit Jupuyter and Colab notebooks and use th cctbxsnip library while doing so.

time management

Track daily writing progress by project in 2024 and 2025

less than 1 minute read

Published:

Most books on writing recommend tracking writing progress, but none address well how to juggle multiple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, manuscript reviews, lectures, and books in parallel. My approach is to track my writing progress on a per-project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progress. The entry of the progress per project requires only a few seconds. I designed the graphs to show the cumulative progress across all projects. Each month has its bar graph. You select the appropriate column and generate the sum to get the cumulative progress for a specific project. I developed this version for 2024 and 2025. I have shared this as an Excel workbook and a Libre Office version on a GitHub repository called writing-progress-2024-25. You can import either into a Google Sheet for faster access.

Track daily writing progress by project in 2023 in an Excel workbook

1 minute read

Published:

A lot of books on writing tout the value of tracking writing progress, but none of them address to my satisfaction how to cope with the problem of juggling mulitple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, and books in parellel. My approach is to track my writing progress on a per project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progess. The graphs are set up to show the cumulative progress across all projects. Each months has its own graph. To get the cummulative progress for a project, you select the appropriate column and the sum will be reported. The entry of the progress per project requires only a few seconds. I have shared this Excel workbook and a Libre Office version on a GitHub repository called writingProgess2023. I have included a webpage where you can paste text into a text area to get the word count. I also have updated the extensive README.md file. I actually import the workbook into Google Sheets and then add the link to my browser toolbar. This gives me instant access to the workbook without the startup time of Excel. This convenience further reduces the motivational barier to updating the project worksheet.

transcription

tree-sitter

Emacs with tree-sitter support

less than 1 minute read

Published:

Tree-sitter is a C library that supports editing code with a concrete syntax tree. This syntax tree enables more powerful editing commands that save time and reduce tedium. Emacs and other leading text editors are still in the process of harnessing tree-sitter.

Emacs must be compiled with the tree-sitter C library already installed on your computer. I provide a protocol for doing so on a fresh installation of Ubuntu 22.04 LTS. I also succeeded with macOS 13.2 (Ventura) after I figured out that I needed to specify the path to the giflib library. Note that this library is different from the tree-sitter.el package that will be built into Emacs version 29.

virtual screening

Targeting RNA structure

less than 1 minute read

Published:

Francis’s dissertation work on targeting RNA structure in drug design was published in the International Journal of Molecular Sciences. He did virutal screening of a vast library on a super computer, machine learning of the leads, molecular dynamics simulations of the lead complexes, and in vitro testing of the binding with microscale thermophoresis.

voice computing

whisper

workshop

MooersLab landing page initiated.

less than 1 minute read

Published:

I discovered that a repo made with the name of a GitHub site can have a README.md file that shows up on the landing page. This file can be used to provide an index or table of contexts to the repos by clustering them by category. This format can draw the visitors attention to relevant repos and is much better than the default tag search approach where the visitor has to know the relevent search terms in advance or has to scroll through all of the repos.

Workshop: Computational Methods in the Structural Sciences

less than 1 minute read

Published:

On the afternoon of Monday, September 26, 2022, Drs Tzanko Doukov and Blaine Mooers co-chaired a four-hour workshop Computational Methods in the Structural Sciences at the annual SSRL/LCLS Users meeting. It had eight speakers from three continents. The topics were quite diverse: micro-ED, cryo-EM, SAXS, radiation damage analysis, solvent channel analysis, and direct phasing. All of the talks were reviting. However, the last speaker really hit a home-run with some very exciting results about extending direct phasing methods. This talk was mentioned several times in other workshops and plenary sessions on the following days.

writing produtivity

writing progress tracking

Track daily writing progress by project in 2024 and 2025

less than 1 minute read

Published:

Most books on writing recommend tracking writing progress, but none address well how to juggle multiple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, manuscript reviews, lectures, and books in parallel. My approach is to track my writing progress on a per-project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progress. The entry of the progress per project requires only a few seconds. I designed the graphs to show the cumulative progress across all projects. Each month has its bar graph. You select the appropriate column and generate the sum to get the cumulative progress for a specific project. I developed this version for 2024 and 2025. I have shared this as an Excel workbook and a Libre Office version on a GitHub repository called writing-progress-2024-25. You can import either into a Google Sheet for faster access.

Track daily writing progress by project in 2023 in an Excel workbook

1 minute read

Published:

A lot of books on writing tout the value of tracking writing progress, but none of them address to my satisfaction how to cope with the problem of juggling mulitple writing projects in parallel. Many academics have to work on manuscripts, grant applications, grant reports, and books in parellel. My approach is to track my writing progress on a per project basis in an Excel workbook that automatically tallies the progress for the day by word count and minutes spent and then updates a bar graph of the cumulative progess. The graphs are set up to show the cumulative progress across all projects. Each months has its own graph. To get the cummulative progress for a project, you select the appropriate column and the sum will be reported. The entry of the progress per project requires only a few seconds. I have shared this Excel workbook and a Libre Office version on a GitHub repository called writingProgess2023. I have included a webpage where you can paste text into a text area to get the word count. I also have updated the extensive README.md file. I actually import the workbook into Google Sheets and then add the link to my browser toolbar. This gives me instant access to the workbook without the startup time of Excel. This convenience further reduces the motivational barier to updating the project worksheet.