A dimensionality reduction technique particularly well suited for visualizing data. (For references, see https://lvdmaaten.github.io/tsne)
The parameters that were used for running t-SNE here are: 50 initial dimensions, perplexity of 30, and theta of 0.5. For datasets with <= 5000 samples, the standard t-SNE algorithm is used. For larger datasets, the Barnes-Hut algorithm is employed.
A dimensionality reduction technique in which the two principal components are chosen to have the largest possible variance.
To analyze relationships between perturbations, we utilize the framework of connectivity. A connectivity score between two perturbations quantifies the similarity of the cellular responses evoked by these perturbations. A score of 1 means that these two perturbations are more similar to each other than 100% of other perturbation pairs. A score of -1 means that these two perturbations are more dissimilar to each other than 100% of other perturbation pairs.
See a heatmap of connections between individual perturbagens in cell lines and all other perturbagens used for the P100 assay or the GCP assay. The tutorial describes the features of the heatmap.
Bring data, in GCT format, from your own P100 or GCP studies to query against our datasets.
Introspect means querying your dataset against itself. Make sure to "Include Introspect" if you would like to see connections within your dataset (in addition to connections between your dataset and Touchstone-P).
In computing connectivity, biological or technical replicates can be aggregated together. Please select which metadata fields should be used to recognize replicates. For example, if you wish to distinguish between different doses of the same compound, make sure to select "pert_dose" (or something similar) as one of the metadata fields by which to group replicates. The possible metadata fields by which to group replicates only appear after you have upload your GCT and selected "Yes" for "Are there replicates in your data?".
Matched mode: When running GUTC, incorporates cell-line information to match
query data against matching cell types in Touchstone. Currently
this includes the following 9 cell types : [A375, A549,
HEPG2, HCC515, HA1E, HT29, MCF7, PC3, VCAP].
Unmatched mode (recommended): When running GUTC, does not incorporate cell-line information when querying
the data against Touchstone signatures.
L-Build ("Light" Build): All levels of L1000 data up to aggregated signatures.
Full Build: All levels of L1000 data up to aggregated signatures, as well as all relevant additional analyses
of the data (Introspect, t-SNE, PCA, etc.).
When querying Touchstone, Feature Space determines what set of genes to query against. When perturbagens are profiled on the L1000 platform, Landmark is recommended. When the queries you wish to use are not landmarks, use BING instead.
Root location within a brew folder that contains the instance matrices and the brew_group folder. Default is brew/pc
List of expected treatment doses in micromolar as a listmaker list. If provided, dose discretization is applied to the pert_dose metadata field to generate a canonicalized pert_idose field. Note this assumes that the pert_dose annotations are in micromolar.
Generates TAS plots and connectivity heatmap of preliminary callibration plates to identify the most suitable experimental conditions of specified parameters. Tool should be run on small pilot experiments, with a variety of experimental parameters such as seeding density and time point. Plots can also be decoupled by parameters such as cell id.
Column filter to sig_build_tool as a listmaker collection
The name of the build used when generating all associated files and folders (e.g. <BUILD_CODE>_metadata). For this reason, the code must be filename compatible.
When merging replicates for L1000, several versions of the merged data are made. This parameter determines which version to use when creating your build. by_rna_well is the default. by_rna_well is recommended.
All data is from the Cancer Cell Line Encyclopedia resource. Expression data was released 15-Aug-2017, copy number data is dated 27-May-2014, and mutational data is dated 15-Aug-2017.
Feature Mapping: Ensembl Ids from the source data were mapped to Entrez Gene Ids using gene annotations from NCBI (downloaded on 02-Mar-2016).
Normalization: RNAseq RPKM values were log2 transformed using log2(max(RPKM, eps)). The data were then normalized
such that the expression values were comparable across cell lines, by minimizing technical variation
and equalizing their distributions (for details of the normalization, see LISS and QNORM entries in the Connectopedia glossary). Post-normalization, the expression values range between 4 and 15 log2 units, with 4 indicating that
a gene is minimally or not expressed and 15 indicating the maximum readout.
Z-scores: The number of standard deviations that a gene is above or below the population mean is called its z-score. The "robust" z-score is resistant to outliers by using median instead of mean and median absolute deviation (MAD) instead of standard deviation. The reference population used to compute the median and MAD for a
particular gene is all CCLE lines with data for that gene.
Z-scores Within Primary Site: Similar to z-scores,
but the reference population used to compute the median and MAD is all CCLE lines from the same lineage with data for that gene.
All scores indicated are in log 2 ratios to reference, binned using the heuristics described in CNVkit.
Deletion: score < -1.1
Loss: -1.1 ≤ score ≤ -0.25
No change: -0.25 < score < +0.2
Gain: +0.2 ≤ score < +0.7
Amplification: +0.7 ≤ score
Access a suite of analysis apps by clicking on the menu (or type command-K to open)
Explore the Connectivity Map by typing here and pressing Enter (see instructions below the search box)
Switch between running a single query and running a batch query.
Give each query a descriptive name that will help you identify your results.
Tip: Each list can have a different number of genes; in fact, you can run a query with only one list (up OR down).
Your query will take about 5 minutes to process; check the History section in the Menu for your results!
Valid genes used in the query have HUGO symbols or Entrez IDs and are well-inferred or directly measured by L1000 (member of the BING gene set). Valid genes not used in a query are those that have a valid HUGO or Entrez identifier but are not part of the BING set. Invalid genes do not have HUGO or Entrez IDs.
Give each query a descriptive name that will help you identify your results.
Your query will take about 5 minutes to process; check the History section in the Menu for your results!
The sig_fastgutc_tool is a reimplementation of our query algorithm that enables faster query results, especially at larger batch sizes. It is the result of crowd-sourced contest. It is currently in beta mode.
Filter datasets by category to see only those of interest.
Data Icons identify published and proprietary datasets.
Click on a row to see a summary of that dataset, including cell lines and treatment conditions, assay type, and dates.
Arrange the table to display the information most important for your work, and add key datasets to favorites.
View details about the collection as a whole and about individual compounds.
View subsets of compounds based on mechanism, drug target, or known disease application.
Purity is assessed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) of compounds after receipt from the vendor.
Status as of publication of this resource (March 2017). We will be updating this but let us know if you notice a discrepancy.
Click on a compound to see details about its structure, mechanism, targets, approval status, and vendor.
Mouse over this graphic to see the classes of proteins targeted by drugs in the hub.
Search CMap for connections. First, search for a perturbagen and check the box to select it. Then view its connections as a list or heatmap.
This is the current count of perturbagens in the reference (touchstone) dataset.
Select data from perturbagens grouped by their MoA or role in the cell.
Choose a perturbagen type, or view them all.
Touchstone is our reference dataset, made from well-annotated perturbagens profiled in a core set of 9 cell lines.
Detailed List is unavailable for Touchstone v1.1.1.1. A new data visualization approach is in development, but to get results in a table format (similar to Detailed View), please click on Heat Map and download the dataset as a GCT file that can be viewed in Excel or similar apps. Please see here for a detailed explanation.
Use the Command app to retrieve the most up-to-date CMap information. Type a slash (/) to see the list of commands available. Select a command, and type the MoA, gene, perturbagen, or other keyword after it to specify your request.
Articles are tagged with topics. Click on a topic tag to see all related articles.
Look it up! A quick reference guide of CMap terms and their meanings.
Email us with your questions.
Click on the heading to read all the articles in this section on a single page, or open each article separately.
Click on a heading to open a menu of articles.
Articles with the same tag(s) as this article can be opened here. To see all articles associated with any tag, click on the tag from the list below.
Each article is tagged with key words that describe its content.
Underlined words link to their definition in the CMap glossary.
Your feedback helps us make Connectopedia more useful.
Average transcriptional impact
TAS is a metric that incorporates the signature strength (the number of significantly differentially expressed transcripts) and signature concordance (the reproducibility of those changes across biological replicates) to capture activity of a compound. The score is computed as the geometric mean of the signature strength and the 75th quantile of pairwise replicate correlations for a given signature. Prior to computing the geometric mean, the signature strength is multiplied by the square root of the number of replicates. This serves to mitigate score shrinkage with increasing replicate number and allows TAS values derived from signatures of different numbers of replicates to be compared with each other.
Signature diversity
Thick black bars signify Transcriptional Activity Scores greater than or equal to 0.5; thinner black bars denote scores less than 0.5. Absence of a bar means no data available. Colored lines (chords) signify similar connectivity scores between cell lines; red for positive connectivity scores of 80-100 (pale to intense color according to the score); blue for negative connectivity. Chords are only shown when TAS scores are > 0.5; thus absence of a chord either means that the perturbagen TAS score is very low, or that no data is available. Chords for individual cell lines can be isolated from the rest of the figure by hovering over the cell line name.
Baseline expression of this gene in each cell line is represented as a z-score (top numbers). Scores were calculated using robust z-score formula:
z-scorei = ( xi - median( X ) )/( MAD( X ) * 1.4826 ),
where:
xi is expression value of a given gene in i-th cell line
X = [ x1, x2 ... xn ] is a vector of expression values for a given gene across n cell lines
MAD( X ) is a median absolute deviation of X
1.4826 is a constant to rescale the score as if the standard deviation of X instead of MAD was used
Median and MAD expression values were calculated using RNA-Seq profiles from a total of 1022 cell lines, comprising data from the Cancer Cell Line Encyclopedia (CCLE; Barretina, et al.) and cell lines nominated by the CMap team. Plots show z-score values only for the core LINCS lines used by CMap in L1000 experiments. Light red or light blue regions indicate positive or negative outlier expression, respectively, of the gene relative to the other lines shown; z-score of a positive outlier in the corresponding cell line is in dark red and a negative outlier is in dark blue.
Summary class connectivity shows a boxplot that summarizes the connectivity of a class. Each data point, shown as a light gray dot, represents the median value of connectivity of one member to the other class members. (This corresponds to the median for each row, excluding the main diagonal, in the heatmap shown below.) The box is the distribution of those data points, where the box boundary represents the interquartile range, the vertical line within the box is the median, and the whiskers reflect the minimum and maximum values of the data (exclusive of extreme outliers, which may appear beyond the whiskers).
Connectivity between members of class is a standard heat map of the connectivity scores, summarized across cell lines, between members of the class, where dark red represents the highest positive scores and deep blue the highest negative scores. Individual scores are revealed to the left below the map by hovering over each cell of the map.
Class inter-cell line connectivity is a plot of the median (black line) and Q25-Q75 connectivity scores (blue area around black line) for each cell line as well as the summary scores across cell lines. In some cases perturbations have not been tested in every cell line; the absence of data is indicated by a “0” for that cell line. The example shown reveals that these estrogen agonists show the strongest connectivity to each other in MCF7, a human breast cancer cell line that expresses the estrogen receptor.
Profile status
Colored portion of top bar indicates the Broad assays in which this compound has been profiled.
L1000 cell/dose coverage
For compounds profiled by L1000, cell lines and dose range for which signatures are available are indicated by dark gray bars (lighter gray bar indicates no data is available for that cell line/dose combination). A bar displayed one row above the 10 uM row indicates that doses higher than 10uM were tested. The 6 rows correspond to 6 canonical doses: 20 nM, 100 nM, 500 nM, 1 uM, 2.5 uM, and 10 uM. (In some cases non-canonical doses were tested; these are rounded to the nearest canonical dose for the purpose of this display. For example, if the dose tested was 3.33uM, the 2.5uM bar is shown in dark gray here.)
Report: OMSI Bus Simulator Activation Key
Introduction
OMSI (Ohne Mauke Simulations-Interface) Bus Simulator is a popular simulation game that allows players to drive buses in a virtual city. The game is known for its realistic graphics and gameplay. However, to access the full features of the game, players need to activate it using a valid activation key. This report provides an overview of the OMSI Bus Simulator activation key, its importance, and the implications of using a cracked or pirated version.
What is an Activation Key?
An activation key is a unique code used to activate a software product, in this case, OMSI Bus Simulator. It verifies that the user has purchased a legitimate copy of the game and allows them to access all its features. The activation key is usually provided by the game developer or retailer and is required to unlock the game's full potential.
Importance of Activation Key
The activation key is essential for several reasons:
- Legitimate Ownership: An activation key ensures that the user has purchased a legitimate copy of the game, which supports the game developers and the gaming industry as a whole.
- Access to Full Features: With an activation key, players can access all the features of the game, including updates, new content, and online multiplayer.
- Security: Activating the game with a valid key helps prevent the use of pirated or cracked versions, which can be malicious and compromise the user's computer security.
Implications of Using a Cracked or Pirated Version
Using a cracked or pirated version of OMSI Bus Simulator, obtained through an unauthorized activation key or no key at all, has several negative consequences:
- Malware Risks: Cracked versions may contain malware or viruses that can harm the user's computer or steal personal data.
- Game Instability: Pirated versions can be unstable, causing crashes, or errors, which can lead to a poor gaming experience.
- No Access to Updates: Users of pirated versions will not receive updates, bug fixes, or new content, which can significantly limit their gaming experience.
- Support for Piracy: Using a cracked version supports piracy, which can harm the game developers and the gaming industry.
How to Obtain a Valid Activation Key
To obtain a valid activation key for OMSI Bus Simulator:
- Purchase from Official Website: Buy the game directly from the official website or authorized retailers.
- Check Retailers: Verify the authenticity of the game and the activation key when purchasing from third-party retailers.
- Avoid Suspicious Sources: Be cautious of suspicious sources offering free or cheap activation keys, as they may be pirated or compromised.
Conclusion
The OMSI Bus Simulator activation key is a crucial component of the gaming experience, ensuring legitimate ownership, access to full features, and security. Using a cracked or pirated version can have negative consequences, including malware risks, game instability, and support for piracy. To enjoy the game without any issues, it is recommended to purchase a valid activation key from authorized sources.
Recommendations
- Always purchase games from official websites or authorized retailers.
- Verify the authenticity of the game and activation key before purchasing.
- Avoid using cracked or pirated versions, as they can compromise computer security and gaming experience.
References
- OMSI Bus Simulator Official Website
- Steam Community Guidelines
- Game Developer Statements on Piracy and Activation Keys
Unlocking the Streets: A Guide to the OMSI 2 Activation Key If you’ve ever wanted to navigate the gritty, hyper-realistic streets of Berlin-Spandau in a double-decker bus, you’ve likely encountered the OMSI 2: Steam Edition
activation process. While the simulation itself is legendary for its depth, getting that activation key
sorted can sometimes feel like trying to stick to a tight bus schedule during rush hour.
Here is everything you need to know about securing and activating your OMSI 2 key. 1. Where to Find Your Key
Depending on where you purchased the game, your activation key will be delivered in different ways: Aerosoft Shop: If you bought directly from the Aerosoft Shop , your serial number is typically included in your confirmation email or visible under "My Downloads" in your account. For those purchasing directly on the Steam Store
, the game is automatically added to your library without needing a manual key entry. Third-Party Retailers: Sites like Gamers-Outlet.net
provide a digital code (CD-key) that you must manually redeem on Steam. 2. How to Activate on Steam Activating your product is straightforward: Launch the client and log in. menu at the top and select "Activate a Product on Steam..." Follow the prompts and enter your
exactly as provided (we recommend using [Ctrl] + [C] and [Ctrl] + [V] to avoid typos!).
Once confirmed, the game will begin downloading automatically. 3. Handling DLC and Add-Ons One of the unique quirks of OMSI 2 is the Aerosoft Launcher
. While the base game usually activates via Steam, some older or third-party add-ons might require activation through the Aerosoft Launcher Admin Rights: Always ensure Steam and OMSI 2 have Administrator rights
on your PC; otherwise, the game might fail to write the activation status to the Windows registry. Offline Activation:
In rare cases, if you have internet connection issues, some installers provide an "Offline Activation" button where you manually enter a local key. 4. Pro-Tip: The "4GB Patch" OMSI 2 Add-On Aachen - Steam
To activate OMSI 2: Bus Simulator , you need an official Steam product key. Once activated, the game is permanently linked to your account, allowing you to download and install it on any compatible PC. How to Activate Your Key
The standard process for activating a digital key bought from retailers like Aerosoft, Gamesplanet, or G2A follows these steps: Open Steam: Launch your Steam client and log in. Add a Game: Click on the "Games" menu at the top. Activate Product: Select "Activate a Product on Steam...".
Enter Code: Follow the prompts and paste your digital key (typically found in your purchase confirmation email) into the input box.
Install: Once activated, the game will appear in your Library. Click "Install" to begin downloading the files. Legitimate Sources for Keys
If you don't own the game yet, you can find official Steam keys at several stores. Avoid "free key" generators, as these are often scams or contain malware.
Official Stores: Aerosoft and Steam are the primary developers and distributors.
Third-Party Retailers: You can often find deals on sites like Eneba, Instant Gaming, and GamersGate. Troubleshooting Common Issues
"Access Denied": If you receive this during installation, retry the process with Administrator rights.
Aerosoft Launcher: Some older DLC or non-Steam versions might require the Aerosoft Launcher for activation. Ensure you have the latest version installed to avoid errors.
Activation Limits: Traditional Aerosoft versions sometimes have a limit of three activations. If you reach this limit due to hardware failures, you may need to contact Aerosoft Support to reset your key.
OMSI 'not activated correctly' - an Aerosoft glitch? - Fellowsfilm
You're looking for a comprehensive guide on "OmSi Bus Simulator Activation Key". I'll provide you with a detailed overview of what it is, its significance, and how to obtain and use it.
What is OmSi Bus Simulator?
OmSi Bus Simulator, also known as OMSI 2, is a popular bus simulation game developed by Marcel Kühne, a German game developer. The game was first released in 2013 and has since become a favorite among simulation game enthusiasts. In OMSI, players take on the role of a bus driver, navigating through a fictional city, transporting passengers, and managing their bus company.
What is an Activation Key?
An activation key, also known as a product key or serial key, is a unique code used to activate and validate a software product, in this case, OmSi Bus Simulator. The activation key is required to unlock the full features of the game, ensuring that only legitimate users can access the game's content.
Why is an Activation Key required?
The activation key serves several purposes:
- Licensing and Validation: The activation key verifies that the user has purchased or obtained a legitimate copy of the game, ensuring that the software is used in accordance with its licensing terms.
- Security: The activation key helps prevent piracy and unauthorized use of the game, protecting the intellectual property rights of the game's developer.
- Feature Unlocking: The activation key unlocks the full features of the game, providing access to all content, updates, and support.
How to Obtain an Activation Key for OmSi Bus Simulator?
There are a few ways to obtain an activation key for OmSi Bus Simulator:
- Purchase from Official Website: You can buy the game directly from the official website of OmSi Bus Simulator. Upon purchase, you'll receive an activation key via email.
- Steam Store: OmSi Bus Simulator is also available on Steam. If you purchase the game on Steam, you'll receive an activation key automatically, and the game will be linked to your Steam account.
- Authorized Retailers: You can also buy the game from authorized retailers, such as online marketplaces or physical game stores. Make sure to check the authenticity of the product and the retailer before making a purchase.
How to Activate OmSi Bus Simulator with an Activation Key?
To activate OmSi Bus Simulator using your activation key, follow these steps:
- Download and Install the Game: If you haven't already, download and install OmSi Bus Simulator from the official website or Steam.
- Launch the Game: Start the game and navigate to the main menu.
- Enter Activation Key: Click on "Settings" or "Options" and look for the "Activation" or "License" section.
- Input Activation Key: Enter your activation key, making sure to type it correctly, and click "Activate" or "Validate".
- Verify Activation: The game will verify your activation key and unlock the full features.
Troubleshooting Common Issues
If you encounter issues with your activation key, here are some common solutions:
- Invalid Activation Key: Double-check that you've entered the activation key correctly. Make sure there are no typos or extra spaces.
- Activation Key Already Used: Ensure that the activation key hasn't been used on another account or device.
- Lost Activation Key: Contact the game's support team or the retailer from which you purchased the game to request a replacement activation key.
Conclusion
In conclusion, the OmSi Bus Simulator activation key is a crucial component of the game, ensuring that only legitimate users can access the game's content. By purchasing the game from authorized sources and following the activation process carefully, you'll be able to enjoy the full features of OmSi Bus Simulator. If you encounter any issues, don't hesitate to reach out to the game's support team for assistance. Happy simulating!
Activating OMSI 2: Bus Simulator is generally straightforward via Steam, though legacy retail versions and specific DLCs may require the Aerosoft Launcher for full registration. 1. Acquisition & Key Types Steam Keys : Most modern digital purchases from official stores like or reputable keyshops like Instant Gaming provide a standard Steam activation code. Aerosoft Serial Keys
: Older physical DVD editions or some standalone DLCs use a unique serial number that must be verified through the Aerosoft Launcher 2. Step-by-Step Activation For Steam (Primary Method) Launch Steam and log into your account. menu and select "Activate a Product on Steam..." Enter your activation key when prompted and follow the on-screen instructions. Once verified, the game will appear in your for download. For Aerosoft Launcher (Legacy/Specific DLCs) Install the Aerosoft Launcher (usually included with the game files or available on the Aerosoft website Navigate to the "Library/Simulation"
Select the product (e.g., OMSI 2 or a specific Add-on) and click "Activate" Enter your email address serial key provided by the retailer. 3. Common Activation Issues Registry Errors : OMSI 2 often requires administrator rights
to write activation data to the Windows Registry. If DLCs show as "not activated" in-game despite being owned, try running the simulator as an administrator. Aerosoft Syncing
: Some users report that Steam-purchased DLCs may not immediately show as "green" (activated) in the Aerosoft Launcher. This is often a visual bug; if the content appears in the OMSI map selection menu, it is working correctly. Hardware Changes
: The Aerosoft Launcher creates a "hardware key" based on your PC components. If you upgrade major parts (like your motherboard), you may need to re-activate the product. aerosoft community services 4. Review Summary Omsi Bus Simulator Manual PDF - Scribd
2. Lack of Updates and Mod Support
OMSI 2 has a massive modding community, featuring maps from all over the world (USA, Hungary, Switzerland, etc.). Most high-quality mods and maps require the game to be running the latest official version. Pirated versions are often stuck on older patches or require complex workarounds to work with community-made content.
What activation keys are
- Definition: Unique alphanumeric codes tied to a software license that unlock the full game.
- Purpose: Prevent piracy, track legitimate ownership, enable updates and DRM features.
Common Issues and Solutions
- Invalid Key: Ensure you've entered the key correctly. Typos are common mistakes.
- Key Already Used: Make sure the key hasn't been used on another account or device.
- Game Not Recognizing Key: Contact the game's support team if the key is valid but not being accepted.
For the Non-Steam (Boxed/Download) Version:
- Install the game from the disc or downloader.
- Open Aerosoft Launcher (installed automatically).
- Click the "Activate Product" plus sign.
- Enter your key. The launcher will phone home to verify it.
- Troubleshooting: If the launcher says "No connection," you may need to install an older version of .NET Framework 3.5 or run the launcher as Administrator.
Unlocking the Ultimate Transit Experience: The Complete Guide to OMSI Bus Simulator Activation Keys
For over a decade, OMSI (Omnibus Simulator) has stood as the gold standard for bus driving simulations. Unlike arcade-style driving games, OMSI offers a gritty, hyper-realistic experience that challenges players to master the intricacies of public transport—from checking tire pressure to selling tickets in pre-announced German currency.
However, for newcomers and veteran simmers alike, one phrase dominates forum threads, Reddit posts, and Steam discussions: "OMSI Bus Simulator activation key."
This guide will walk you through everything you need to know about activation keys for both OMSI 1 and OMSI 2, how to avoid scams, where to buy legitimate keys, and how to troubleshoot common activation errors.
Importance of Using a Genuine Activation Key
Using a genuine OMSI Bus Simulator activation key is crucial for several reasons:
-
Full Access to Game Features: A valid key unlocks all the features of the game, providing an immersive and complete gaming experience.
-
Support for Developers: Purchasing an activation key supports the developers, encouraging them to continue updating the game and releasing new content.
-
Avoiding Malware: Pirated keys or cracks can expose your computer to malware and viruses, compromising your data and system security.
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