Mendely: Collections versus Groups

 In Mendeley, a popular reference management software, "Collections" and "Groups" serve different purposes for organizing and sharing references. Here's a detailed comparison:

Collections

• Purpose: Collections are used to organize your personal library of references into specific categories or topics.
• Visibility: Only you can see and manage your collections. They are private and are not shared with others unless you explicitly share them.
• Usage: You can create multiple collections to sort your references based on projects, research topics, or any other criteria that suit your needs.
• Management: You can add references to multiple collections, and a reference can belong to more than one collection at the same time.
• Synonym: Collections are sometimes referred to as "folders" in other reference management systems.

Groups

• Purpose: Groups are used for collaboration and sharing references with others.
• Visibility: Depending on the group type, references in groups can be visible to members only (private groups), anyone with the link (invite-only groups), or everyone (public groups).
• Usage: You can create groups for different collaborative projects, where all members can add and manage references. This is particularly useful for research teams, academic classes, or any collaborative work.
• Management: Groups have a social component, where members can discuss references, share notes, and collaborate directly within Mendeley.
• Types of Groups:
  • Private Groups: Only invited members can join and see the content.
  • Invite-Only Groups: Anyone can see the group, but they need an invitation to join and view content.
  • Public Groups: Anyone can join and view the content without an invitation.

Summary

• Collections are for personal organization and are private to the user.
• Groups are for collaboration and sharing, with different visibility options based on the type of group.

Understanding these differences helps you effectively manage your references and collaborate with others using Mendeley.

Freyja

 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.

https://github.com/andersen-lab/Freyja

from alignment to snp

https://www.researchgate.net/post/Does_anyone_know_a_software_for_SNPs_analysis_from_FASTA_sequences

screencast software, OBS, windows, mac, linux

screencast software, OBS, windows, mac, linux

https://obsproject.com/welcome

secure and anonymous doodle for voting

using email to vote (each email vote once)
https://www.adoodle.org/index.php

UTC adobe creative cloud, acrobat DC installation

Obtaining Creative Cloud – Start Here

acrobat professional version
https://blog.utc.edu/it-knowledge-base/obtaining-creative-cloud-utc-employees/

The APPs include Photoshop, Illustrator, Acrobat DC,

list of CFU analysis software

open CFU
https://sourceforge.net/projects/opencfu/files/linux/

https://www.nature.com/articles/s41598-018-24916-9

biomedical data tools

https://commonfund.nih.gov/bd2k/resources#Indexing

data privacy

• PrivaSeq(link is external): A tool base for quantification and analysis of the individual characterizing information leakage, which can be used to link phenotype datasets to genotype datasets and reveal sensitive information in linking attacks.
• PopMedNet(link is external): A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks.
• PeerSMC(link is external): A web-browser based tool allowing for two or more parties to conduct secure multiparty computation. 

The data visualization awards are making a wide range of large biomedical datasets easier to use and interpret, including brain scan imaging, geo-referenced data, health care systems dynamic data, and genomics data.

• GGV(link is external): The Geography of Genetic Variants (GGV) browser is a web services software implementation of EEMS. EEMS is a new and innovative method for visualizing and analyzing population genetics data and other such geo-tagged biomedical data.
• HSD ontology(link is external): A novel method for identifying and extracting healthcare systems dynamics (HSD) data, and for integrating these data with "traditional" electronic health record (EHR) data. HSD data take into account the dynamics of the healthcare system when interpreting medical records. (For example, the date when a patient developed a disease can be inferred from when they received a diagnosis, scheduled a doctor visit, tests were ordered, etc.)
• Caleydo Web(link is external): Caleydo Web is a suite of web based methods and software tools designed to meet current needs for visualization and analysis of complex, heterogeneous biomedical data.
• Vials(link is external): Vials is a novel visual analysis tool for analyzing splicing patterns in RNA-seq data

The data wrangling awards are developing new methods and tools to improve the utility of big datasets by making them easier to share, integrate, and transform.

• IRRMC(link is external): The Integrated Resource for Reproducibility in Macromolecular Crystallography is a public database of x ray crystallography data, which provides a method for cleaning, collecting, and providing metadata for raw x-ray diffraction datasets.
• Fitmunk(link is external): A new program for the automatic building of amino-acid side chains in protein crystal structures.
• MODMatcher(link is external): A computational approach to identify and correct sample labeling errors in the multiple types of molecular data that can be used in subsequent integrative analyses.
• ActMiR(link is external): A software tool that infers the activity of miRNAs from expression data of target genes.
• AutoEEG(link is external) and MERCuRY: New methods to process EEG cohort datasets and clinical records, align epileptic events, and identify seizure onset patterns that are of direct impact to clinicians studying epilepsy.
• Mygeneinfo.com(link is external) and myvarientinfo.com: Open source, high-performance, and continuously-updated data application programming interfaces (APIs) for accessing comprehensive, structured gene and variant annotations. The integration of multiple information streams into a community platform for annotating gene and genetic variation data significantly reduces siloing and duplication of effort across multiple databases and their user communities.
• AsterixDB(link is external): A data management tool enabling ready access to and use of behavioral and other health-relevant data contained in social media streams developed primarily for HIV risk behavioral research.
• geQTL(link is external): A sparse regression method that can detect both group-wise and individual associations between SNPs and expression traits.

PSORT WWW Server

PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin, e.g., Gram-negative bacteria, as inputs. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information.

https://psort.hgc.jp/

Cytosim.org

Nedelec lab, EMBL
http://www.cytosim.org/

Mogilner lab codes

https://cims.nyu.edu/~mogilner/codes.html

network software

=> RTN, bioconductor

https://bioconductor.org/packages/release/bioc/html/RTN.html

=> KEGGREST
http://bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.R


=> Cytoscape


=> KENev



=> MARINa (MATlab)

=> ingenuity

=> geneXplain

JAX computational genomics tools

On the academic side:

We will be using a number of genomic analysis software packages/tools. Please try to download and install the tools/programs listed below (IGV, R/RStudio and Python).  Ada Zhan (cc’ed here) can assist you with installation questions. We will also be able to provide support on the first day of the course. We will use a cloud computing environment (web-based) but you will get information on that platform just before the course.

If you do not have a laptop at your disposal please alert me ASAP so that we can prepare a machine for your use.

Please install the following:

Integrative Genomics Viewer: (IGV) (Broad Institute)

Please go to the Broad institute website here and download the IGV version for your Mac or PC.

R:

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio   To install on:

Windows:

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Mac OS X:

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux:

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the  RStudio IDE.

Python:  To set  up Python:

Python is a popular language for scientific computing and data science, as well as being a great for general-purpose programming. Installing all of the scientific packages individually can be a bit difficult, so we recommend an using an all-in-one installer, like Anaconda.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

• Download and install Anaconda.
• Download the default Python 3 installer. Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

• Download and install Anaconda.
• Download the default Python 3 installer. Use all of the defaults for installation.

Linux

We recommend the all-in-one scientific Python installerAnaconda.

1. Download the installer that matches your operating system and save it in your home folder. Download the default Python 3 installer.
2. Open a terminal window.
3. Type

bash Anaconda-

and then press tab. The name of the file you just downloaded should appear.

4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

applejack, install keras

See https://keras.io/#installation

sudo pip install keras

flow charts software for education

Sent by JD

Raptor ( http://raptor.martincarlisle.com/ )

Runs on Windows. There is apparently a version for Ubuntu Linux that

doesn't have all the features. May be runnable on a Mac using Wine or

other Windows emulation software. No support for iOS. Can do

object-oriented flowcharting and can generate Java code. Doesn't appear

to have the graphical capabilities of Visual Logic.

Flowgorithm ( http://www.flowgorithm.org/ )

Runs on Windows. Will generate code in a number of high-level languages,

but can execute directly from the flowchart like Visual Logic.

LARP ( http://larp.marcolavoie.ca/en/default.htm )

Runs on Windows. Looks to be more of a pseudocode-type language, but

generates flowcharts.

None of the above appears to be runnable on iOS devices (we discussed

the desirability of being able to run on iPads). So far, the only

similar product I have found that runs on iOS is Hopscotch:

https://www.gethopscotch.com/

It is intended to give kids exposure to coding concepts. I'm not sure if

it can do all the same things as Visual Logic. Does anyone else have

experience with it?

annaconda py2.7 commandline installation, applejack

laptop: applejack,

Download commandline Anaconda2 installation using python 2.7.

Under 'hqin'
bash Anaconda2-4.2.0-MacOSX-x86_64.sh

Anaconda2 will now be installed into this location:

/Users/hqin/anaconda2

wine, osX installation, Visual Logic run

Based on the instructions of
https://www.davidbaumgold.com/tutorials/wine-mac/#part-1:-install-homebrew
The whole installation process probably took 1-2 hours, depending on network speed.

First, install homebrew (a package manager)

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

brew doctor

Warning: Your Xcode (6.2) is outdated.

Please update to Xcode 7.2.1 (or delete it).

Xcode can be updated from the App Store

brew tap caskroom/cask

Byte-5:~ hqin$ brew tap caskroom/cask

==> Tapping caskroom/cask

Cloning into '/usr/local/Homebrew/Library/Taps/caskroom/homebrew-cask'...

remote: Counting objects: 3616, done.

remote: Compressing objects: 100% (3601/3601), done.

remote: Total 3616 (delta 34), reused 267 (delta 11), pack-reused 0

Receiving objects: 100% (3616/3616), 1.19 MiB | 0 bytes/s, done.

Resolving deltas: 100% (34/34), done.

Checking connectivity... done.

Tapped 0 formulae (3,624 files, 3.7M)

brew cask install java xquartz

Byte-5:~ hqin$ brew cask install java xquartz

==> Creating Caskroom at /usr/local/Caskroom

==> We'll set permissions properly so we won't need sudo in the future

Password:

==> Caveats

This Cask makes minor modifications to the JRE to prevent issues with

packaged applications, as discussed here:

  https://bugs.eclipse.org/bugs/show_bug.cgi?id=411361

If your Java application still asks for JRE installation, you might need

to reboot or logout/login.

Installing this Cask means you have AGREED to the Oracle Binary Code

License Agreement for Java SE at

  https://www.oracle.com/technetwork/java/javase/terms/license/index.html

==> Downloading http://download.oracle.com/otn-pub/java/jdk/8u112-b16/jdk-8u112-

######################################################################## 100.0%

==> Verifying checksum for Cask java

==> Running installer for java; your password may be necessary.

==> Package installers may write to any location; options such as --appdir are i

==> installer: Package name is JDK 8 Update 112

==> installer: Upgrading at base path /

==> installer: The upgrade was successful.

🍺  java was successfully installed!

==> Downloading https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.11.dmg

######################################################################## 100.0%

==> Verifying checksum for Cask xquartz

==> Running installer for xquartz; your password may be necessary.

==> Package installers may write to any location; options such as --appdir are ignored.

==> Verifying checksum for Cask xquartz

==> Running installer for xquartz; your password may be necessary.

==> Package installers may write to any location; options such as --appdir are ignored.

==> installer: Package name is XQuartz 2.7.11

==> installer: Upgrading at base path /

==> installer: The upgrade was successful.

==> /Library/LaunchAgents/org.macosforge.xquartz.startx.plist: Operation already in progress

🍺  xquartz was successfully installed!

brew install wine

Byte-5:~ hqin$ brew install wine

==> Installing dependencies for wine: libpng, freetype, jpeg, pkg-config, libtool, libusb, libusb-compat, fontconfig, libtiff, webp, gd, libgphoto2, little-cms2, cmake, jasper, libicns, makedepend, openssl, net-snmp, sane-backends, libtasn1, gmp, nettle, libffi, p11-kit, gnutls

==> Installing wine dependency: libpng

==> Using the sandbox

==> Downloading ftp://ftp.simplesystems.org/pub/libpng/png/src/libpng16/libpng-1.6.28.tar.xz

######################################################################## 100.0%

==> ./configure --disable-silent-rules --prefix=/usr/local/Cellar/libpng/1.6.28

==> make

==> make test

==> make install

🍺  /usr/local/Cellar/libpng/1.6.28: 26 files, 1.7M, built in 4 minutes 26 seconds

==> Installing wine dependency: freetype

==> Downloading https://downloads.sf.net/project/freetype/freetype2/2.7.1/freetype-2.7.1.tar.bz2

==> Downloading from https://iweb.dl.sourceforge.net/project/freetype/freetype2/2.7.1/freetype-2.7.1.tar

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/freetype/2.7.1 --without-harfbuzz

==> make

==> make install

🍺  /usr/local/Cellar/freetype/2.7.1: 62 files, 3.7M, built in 1 minute 5 seconds

==> Installing wine dependency: jpeg

==> Downloading http://www.ijg.org/files/jpegsrc.v8d.tar.gz

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/jpeg/8d

==> make install

🍺  /usr/local/Cellar/jpeg/8d: 20 files, 1.3M, built in 29 seconds

==> Installing wine dependency: pkg-config

==> Downloading https://homebrew.bintray.com/bottles/pkg-config-0.29.1_2.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring pkg-config-0.29.1_2.yosemite.bottle.tar.gz

🍺  /usr/local/Cellar/pkg-config/0.29.1_2: 10 files, 627.4K

==> Installing wine dependency: libtool

==> Downloading https://ftpmirror.gnu.org/libtool/libtool-2.4.6.tar.xz

==> Downloading from http://open-source-box.org/libtool/libtool-2.4.6.tar.xz

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/libtool/2.4.6_1 --program-prefix=g --enable-ltdl-install

==> make install

==> Caveats

In order to prevent conflicts with Apple's own libtool we have prepended a "g"

so, you have instead: glibtool and glibtoolize.

==> Summary

🍺  /usr/local/Cellar/libtool/2.4.6_1: 71 files, 3.7M, built in 45 seconds

==> Installing wine dependency: libusb

==> Downloading https://github.com/libusb/libusb/releases/download/v1.0.20/libusb-1.0.20.tar.bz2

==> Downloading from https://github-cloud.s3.amazonaws.com/releases/15120676/80d0f5e8-5a3e-11e5-82a6-d21

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/libusb/1.0.20

==> make install

🍺  /usr/local/Cellar/libusb/1.0.20: 28 files, 754.7K, built in 23 seconds

==> Installing wine dependency: libusb-compat

==> Downloading https://downloads.sourceforge.net/project/libusb/libusb-compat-0.1/libusb-compat-0.1.5/l

==> Downloading from https://pilotfiber.dl.sourceforge.net/project/libusb/libusb-compat-0.1/libusb-compa

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/libusb-compat/0.1.5

==> make install

🍺  /usr/local/Cellar/libusb-compat/0.1.5: 14 files, 136.6K, built in 16 seconds

==> Installing wine dependency: fontconfig

==> Downloading https://www.freedesktop.org/software/fontconfig/release/fontconfig-2.12.1.tar.bz2

######################################################################## 100.0%

==> Downloading https://raw.githubusercontent.com/Homebrew/formula-patches/3790bcd/fontconfig/patch-2.12

######################################################################## 100.0%

==> Patching

==> Applying patch-2.12.1-fccache.diff

patching file src/fccache.c

==> ./configure --disable-silent-rules --enable-static --with-add-fonts=/System/Library/Fonts,/Library/F

==> make install RUN_FC_CACHE_TEST=false

==> Regenerating font cache, this may take a while

==> /usr/local/Cellar/fontconfig/2.12.1_2/bin/fc-cache -frv

^[[B^[[B🍺  /usr/local/Cellar/fontconfig/2.12.1_2: 469 files, 3.8M, built in 2 minutes 36 seconds

==> Installing wine dependency: libtiff

==> Downloading http://download.osgeo.org/libtiff/tiff-4.0.7.tar.gz

######################################################################## 100.0%

==> Downloading https://mirrors.ocf.berkeley.edu/debian/pool/main/t/tiff/tiff_4.0.7-4.debian.tar.xz

######################################################################## 100.0%

==> Patching

==> Applying patches/01-CVE.patch

patching file ChangeLog

patching file libtiff/tif_read.c

patching file libtiff/tiffiop.h

==> Applying patches/02-CVE.patch

patching file ChangeLog

patching file tools/tiffcp.c

==> Applying patches/03-CVE.patch

patching file ChangeLog

patching file libtiff/tif_luv.c

patching file libtiff/tif_pixarlog.c

==> Applying patches/04-CVE.patch

patching file ChangeLog

patching file libtiff/tif_dirread.c

patching file libtiff/tif_strip.c

==> Applying patches/05-CVE.patch

patching file ChangeLog

patching file libtiff/tif_ojpeg.c

==> Applying patches/06-CVE.patch

patching file ChangeLog

patching file tools/tiffcrop.c

==> Applying patches/07-CVE.patch

patching file ChangeLog

patching file tools/tiffcrop.c

==> Applying patches/08-CVE.patch

patching file ChangeLog

patching file tools/tiffcrop.c

==> Applying patches/09-CVE.patch

patching file ChangeLog

patching file tools/tiffinfo.c

==> Applying patches/10-CVE.patch

patching file ChangeLog

patching file tools/tiffcp.c

==> Applying patches/11-CVE.patch

patching file ChangeLog

patching file libtiff/tif_dir.c

==> Applying patches/12-CVE.patch

patching file ChangeLog

patching file tools/tiffcp.c

==> Applying patches/13-CVE.patch

patching file ChangeLog

patching file tools/tiffcp.c

==> Applying patches/14-CVE.patch

patching file ChangeLog

patching file tools/tiffcp.c

==> Applying patches/15-TIFFFaxTabEnt_bugfix.patch

patching file ChangeLog

patching file libtiff/tif_fax3.h

==> Applying patches/16-CVE-2016-10094.patch

patching file ChangeLog

patching file tools/tiff2pdf.c

==> ./configure --prefix=/usr/local/Cellar/libtiff/4.0.7_1 --without-x --with-jpeg-include-dir=/usr/loca

==> make install

🍺  /usr/local/Cellar/libtiff/4.0.7_1: 248 files, 5.0M, built in 57 seconds

==> Installing wine dependency: webp

==> Downloading http://downloads.webmproject.org/releases/webp/libwebp-0.5.2.tar.gz

######################################################################## 100.0%

==> ./configure --disable-gl --enable-libwebpmux --enable-libwebpdemux --enable-libwebpdecoder --prefix=

==> make install

🍺  /usr/local/Cellar/webp/0.5.2: 35 files, 3.3M, built in 43 seconds

==> Installing wine dependency: gd

==> Downloading https://github.com/libgd/libgd/releases/download/gd-2.2.3/libgd-2.2.3.tar.xz

==> Downloading from https://github-cloud.s3.amazonaws.com/releases/29669711/611ef3ba-4ffe-11e6-9382-af2

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/gd/2.2.3_1 --without-x --without-xpm --with-png=/usr/local/op

==> make install

🍺  /usr/local/Cellar/gd/2.2.3_1: 36 files, 2.1M, built in 29 seconds

==> Installing wine dependency: libgphoto2

==> Downloading https://downloads.sourceforge.net/project/gphoto/libgphoto/2.5.12/libgphoto2-2.5.12.tar.

==> Downloading from https://superb-dca2.dl.sourceforge.net/project/gphoto/libgphoto/2.5.12/libgphoto2-2

######################################################################## 100.0%

==> ./configure --disable-silent-rules --prefix=/usr/local/Cellar/libgphoto2/2.5.12

==> make install

🍺  /usr/local/Cellar/libgphoto2/2.5.12: 169 files, 7.5M, built in 1 minute 40 seconds

==> Installing wine dependency: little-cms2

==> Downloading https://downloads.sourceforge.net/project/lcms/lcms/2.8/lcms2-2.8.tar.gz

==> Downloading from https://pilotfiber.dl.sourceforge.net/project/lcms/lcms/2.8/lcms2-2.8.tar.gz

######################################################################## 100.0%

tar: copyfile unpack (lcms2-2.8/Projects/mac/.DS_Store) failed: File exists

==> ./configure --prefix=/usr/local/Cellar/little-cms2/2.8

==> make install

🍺  /usr/local/Cellar/little-cms2/2.8: 18 files, 1.9M, built in 38 seconds

==> Installing wine dependency: cmake

==> Downloading https://homebrew.bintray.com/bottles/cmake-3.7.1.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring cmake-3.7.1.yosemite.bottle.tar.gz

==> Caveats

Emacs Lisp files have been installed to:

  /usr/local/share/emacs/site-lisp/cmake

==> Summary

🍺  /usr/local/Cellar/cmake/3.7.1: 2,143 files, 29.3M

==> Installing wine dependency: jasper

==> Downloading https://github.com/mdadams/jasper/archive/version-2.0.10.tar.gz

==> Downloading from https://codeload.github.com/mdadams/jasper/tar.gz/version-2.0.10

######################################################################## 100.0%

==> cmake .. -DGLUT_glut_LIBRARY=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/De

==> make

==> make test

==> make install

🍺  /usr/local/Cellar/jasper/2.0.10: 39 files, 1.3M, built in 49 seconds

==> Installing wine dependency: libicns

==> Downloading https://downloads.sourceforge.net/project/icns/libicns-0.8.1.tar.gz

==> Downloading from https://superb-sea2.dl.sourceforge.net/project/icns/libicns-0.8.1.tar.gz

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/libicns/0.8.1_3

==> make install

🍺  /usr/local/Cellar/libicns/0.8.1_3: 19 files, 421.0K, built in 22 seconds

==> Installing wine dependency: makedepend

==> Downloading https://homebrew.bintray.com/bottles/makedepend-1.0.5.yosemite.bottle.1.tar.gz

######################################################################## 100.0%

==> Pouring makedepend-1.0.5.yosemite.bottle.1.tar.gz

🍺  /usr/local/Cellar/makedepend/1.0.5: 7 files, 72.7K

==> Installing wine dependency: openssl

==> Downloading https://www.openssl.org/source/openssl-1.0.2j.tar.gz

######################################################################## 100.0%

==> make clean

==> perl ./Configure --prefix=/usr/local/Cellar/openssl/1.0.2j --openssldir=/usr/local/etc/openssl no-ss

==> make depend

==> make

==> make test

==> make clean

==> perl ./Configure --prefix=/usr/local/Cellar/openssl/1.0.2j --openssldir=/usr/local/etc/openssl no-ss

==> make depend

==> make

==> make test

==> make install MANDIR=/usr/local/Cellar/openssl/1.0.2j/share/man MANSUFFIX=ssl

==> lipo -create build-x86_64/libcrypto.1.0.0.dylib build-i386/libcrypto.1.0.0.dylib -output /usr/local/

==> lipo -create build-x86_64/libcrypto.a build-i386/libcrypto.a -output /usr/local/Cellar/openssl/1.0.2

==> lipo -create build-x86_64/libssl.1.0.0.dylib build-i386/libssl.1.0.0.dylib -output /usr/local/Cellar

==> lipo -create build-x86_64/libssl.a build-i386/libssl.a -output /usr/local/Cellar/openssl/1.0.2j/lib/

==> lipo -create build-x86_64/engines/lib4758cca.dylib build-i386/engines/lib4758cca.dylib -output /usr/

==> lipo -create build-x86_64/engines/libaep.dylib build-i386/engines/libaep.dylib -output /usr/local/Ce

==> lipo -create build-x86_64/engines/libatalla.dylib build-i386/engines/libatalla.dylib -output /usr/lo

==> lipo -create build-x86_64/engines/libcapi.dylib build-i386/engines/libcapi.dylib -output /usr/local/

==> lipo -create build-x86_64/engines/libchil.dylib build-i386/engines/libchil.dylib -output /usr/local/

==> lipo -create build-x86_64/engines/libcswift.dylib build-i386/engines/libcswift.dylib -output /usr/lo

==> lipo -create build-x86_64/engines/libgmp.dylib build-i386/engines/libgmp.dylib -output /usr/local/Ce

==> lipo -create build-x86_64/engines/libgost.dylib build-i386/engines/libgost.dylib -output /usr/local/

==> lipo -create build-x86_64/engines/libnuron.dylib build-i386/engines/libnuron.dylib -output /usr/loca

==> lipo -create build-x86_64/engines/libpadlock.dylib build-i386/engines/libpadlock.dylib -output /usr/

==> lipo -create build-x86_64/engines/libsureware.dylib build-i386/engines/libsureware.dylib -output /us

==> lipo -create build-x86_64/engines/libubsec.dylib build-i386/engines/libubsec.dylib -output /usr/loca

==> lipo -create build-x86_64/openssl build-i386/openssl -output /usr/local/Cellar/openssl/1.0.2j/bin/op

==> Caveats

A CA file has been bootstrapped using certificates from the SystemRoots

keychain. To add additional certificates (e.g. the certificates added in

the System keychain), place .pem files in

  /usr/local/etc/openssl/certs

and run

  /usr/local/opt/openssl/bin/c_rehash

This formula is keg-only, which means it was not symlinked into /usr/local.

Apple has deprecated use of OpenSSL in favor of its own TLS and crypto libraries

Generally there are no consequences of this for you. If you build your

own software and it requires this formula, you'll need to add to your

build variables:

    LDFLAGS:  -L/usr/local/opt/openssl/lib

    CPPFLAGS: -I/usr/local/opt/openssl/include

    PKG_CONFIG_PATH: /usr/local/opt/openssl/lib/pkgconfig

==> Summary

🍺  /usr/local/Cellar/openssl/1.0.2j: 1,696 files, 17.8M, built in 10 minutes 45 seconds

==> Installing wine dependency: net-snmp

==> Downloading https://homebrew.bintray.com/bottles/net-snmp-5.7.3.yosemite.bottle.3.tar.gz

######################################################################## 100.0%

==> Pouring net-snmp-5.7.3.yosemite.bottle.3.tar.gz

==> Caveats

This formula is keg-only, which means it was not symlinked into /usr/local.

macOS already provides this software and installing another version in

parallel can cause all kinds of trouble.

Generally there are no consequences of this for you. If you build your

own software and it requires this formula, you'll need to add to your

build variables:

    LDFLAGS:  -L/usr/local/opt/net-snmp/lib

    CPPFLAGS: -I/usr/local/opt/net-snmp/include

==> Summary

🍺  /usr/local/Cellar/net-snmp/5.7.3: 538 files, 12.8M

==> Installing wine dependency: sane-backends

==> Downloading https://fossies.org/linux/misc/sane-backends-1.0.25.tar.gz

######################################################################## 100.0%

==> Downloading https://raw.githubusercontent.com/Homebrew/formula-patches/6dd7790c/sane-backends/1.0.25

######################################################################## 100.0%

==> Patching

==> Applying 1.0.25-missing-types.patch

patching file backend/pieusb_buffer.c

patching file include/sane/sane.h

patching file include/sane/sanei_backend.h

patching file sanei/sanei_ir.c

patch unexpectedly ends in middle of line

Hunk #1 succeeded at 29 with fuzz 1.

==> ./configure --prefix=/usr/local/Cellar/sane-backends/1.0.25_1 --localstatedir=/usr/local/var --witho

==> make

==> make install

🍺  /usr/local/Cellar/sane-backends/1.0.25_1: 428 files, 19.9M, built in 3 minutes 22 seconds

==> Installing wine dependency: libtasn1

==> Downloading https://ftpmirror.gnu.org/libtasn1/libtasn1-4.9.tar.gz

==> Downloading from http://mirror.thecodefactory.org/gnu/libtasn1/libtasn1-4.9.tar.gz

######################################################################## 100.0%

==> ./configure --prefix=/usr/local/Cellar/libtasn1/4.9 --disable-silent-rules

==> make install

🍺  /usr/local/Cellar/libtasn1/4.9: 59 files, 674.4K, built in 59 seconds

==> Installing wine dependency: gmp

==> Downloading https://homebrew.bintray.com/bottles/gmp-6.1.2.yosemite.bottle.1.tar.gz

######################################################################## 100.0%

==> Pouring gmp-6.1.2.yosemite.bottle.1.tar.gz

🍺  /usr/local/Cellar/gmp/6.1.2: 18 files, 3.1M

==> Installing wine dependency: nettle

==> Downloading https://homebrew.bintray.com/bottles/nettle-3.3.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring nettle-3.3.yosemite.bottle.tar.gz

🍺  /usr/local/Cellar/nettle/3.3: 81 files, 2.0M

==> Installing wine dependency: libffi

==> Downloading https://homebrew.bintray.com/bottles/libffi-3.0.13.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring libffi-3.0.13.yosemite.bottle.tar.gz

==> Caveats

This formula is keg-only, which means it was not symlinked into /usr/local.

Some formulae require a newer version of libffi.

Generally there are no consequences of this for you. If you build your

own software and it requires this formula, you'll need to add to your

build variables:

    LDFLAGS:  -L/usr/local/opt/libffi/lib

    PKG_CONFIG_PATH: /usr/local/opt/libffi/lib/pkgconfig

==> Summary

🍺  /usr/local/Cellar/libffi/3.0.13: 15 files, 377.2K

==> Installing wine dependency: p11-kit

==> Downloading https://homebrew.bintray.com/bottles/p11-kit-0.23.3.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring p11-kit-0.23.3.yosemite.bottle.tar.gz

🍺  /usr/local/Cellar/p11-kit/0.23.3: 59 files, 855.4K

==> Installing wine dependency: gnutls

==> Downloading https://homebrew.bintray.com/bottles/gnutls-3.4.17_1.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring gnutls-3.4.17_1.yosemite.bottle.tar.gz

🍺  /usr/local/Cellar/gnutls/3.4.17_1: 1,117 files, 7.3M

==> Installing wine 

==> Downloading https://homebrew.bintray.com/bottles/wine-1.8.6.yosemite.bottle.tar.gz

######################################################################## 100.0%

==> Pouring wine-1.8.6.yosemite.bottle.tar.gz

==> Caveats

You may want to get winetricks:

  brew install winetricks

By default Wine uses a native Mac driver. To switch to the X11 driver, use

regedit to set the "graphics" key under "HKCUSoftwareWineDrivers" to

"x11" (or use winetricks).

For best results with X11, install the latest version of XQuartz:

  https://xquartz.macosforge.org/

==> Summary

🍺  /usr/local/Cellar/wine/1.8.6: 2,506 files, 261.2M

Byte-5:~ hqin$ 

Some behind-the-scence running jobs:

Byte-5:~ hqin$ ps

  PID TTY           TIME CMD

46331 ttys000    0:00.03 -bash

48818 ttys000    0:24.31 /System/Library/Frameworks/Ruby.framework/Versions/Current/usr/bin/ruby -W0 /u

53010 ttys000    0:00.01 /System/Library/Frameworks/Ruby.framework/Versions/Current/usr/bin/ruby -W0 /u

53012 ttys000    0:00.54 /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby -W0 -I /us

74320 ttys000    0:00.02 /Applications/Xcode.app/Contents/Developer/usr/bin/make

76833 ttys000    0:00.00 /bin/sh -c dir=test; target=all; if expr " crypto ssl engines apps test tools 

76835 ttys000    0:00.00 /bin/sh -c dir=test; target=all; if expr " crypto ssl engines apps test tools 

76836 ttys000    0:00.05 /Applications/Xcode.app/Contents/Developer/usr/bin/make -e LC_ALL=C PLATFORM=d

77274 ttys000    0:00.00 /System/Library/Frameworks/Ruby.framework/Versions/Current/usr/bin/ruby -x /us

48266 ttys001    0:00.02 -bash

Byte-5:~ hqin$ which wine

/usr/local/bin/wine

Can I run VisualLogic on osX now?

Byte-5:windows hqin$ wine VisualLogic-Course-2.2.10.exe 

Yes, it worked.

More References: 
http://stackoverflow.com/questions/39065921/what-do-raw-githubusercontent-com-urls-represent